diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..89e9080 --- /dev/null +++ b/.gitignore @@ -0,0 +1,13 @@ +client_secrets*.json +.idea +*.iml +target +.classpath +.project +.settings +bin +*~ +lib/bwa-0.7.9a +.metadata +*TestPipeline.java +.Rproj.user diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..179367d --- /dev/null +++ b/.travis.yml @@ -0,0 +1,11 @@ +language: java + +jdk: + - oraclejdk8 + - oraclejdk7 + - openjdk7 + +script: mvn test javadoc:javadoc + +after_success: + - mvn clean cobertura:cobertura -Dcobertura.report.format=xml coveralls:cobertura \ No newline at end of file diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst new file mode 100644 index 0000000..35f06d6 --- /dev/null +++ b/CONTRIBUTING.rst @@ -0,0 +1,75 @@ +How to contribute +=================================== + +First of all, thank you for contributing! + +The mailing list +---------------- + +For general questions or if you are having trouble getting started, try the +`Google Genomics Discuss mailing list `_. +It's a good way to sync up with other people who use googlegenomics including the core developers. You can subscribe +by sending an email to ``google-genomics-discuss+subscribe@googlegroups.com`` or just post using +the `web forum page `_. + + +Local development +----------------- + +With Maven you can locally install a SNAPSHOT version of the code, to use from other projects +directly without having to wait for the Maven repository. Use: + +`mvn install` + +to run the full tests and do a local install. You can also use + +`mvn install -DskipITs` + +to run only the unit tests and do a local install. This is faster. + +Submitting issues +----------------- + +If you are encountering a bug in the code or have a feature request in mind - file away! + + +Submitting a pull request +------------------------- + +If you are ready to contribute code, Github provides a nice `overview on how to create a pull request +`_. + +Some general rules to follow: + +* Do your work in `a fork `_ of this repo. +* Create a branch for each update that you're working on. + These branches are often called "feature" or "topic" branches. Any changes + that you push to your feature branch will automatically be shown in the pull request. +* Keep your pull requests as small as possible. Large pull requests are hard to review. + Try to break up your changes into self-contained and incremental pull requests. +* The first line of commit messages should be a short (<80 character) summary, + followed by an empty line and then any details that you want to share about the commit. +* Please try to follow the existing syntax style + +When you submit or change your pull request, the Travis build system will automatically run tests. +If your pull request fails to pass tests, review the test log, make changes and +then push them to your feature branch to be tested again. + + +Contributor License Agreements +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +All pull requests are welcome. Before we can submit them though, there is a legal hurdle we have to jump. +You'll need to fill out either the individual or corporate Contributor License Agreement +(CLA). + +* If you are an individual writing original source code and you're sure you + own the intellectual property, then you'll need to sign an `individual CLA + `_. +* If you work for a company that wants to allow you to contribute your work, + then you'll need to sign a `corporate CLA + `_. + +Follow either of the two links above to access the appropriate CLA and +instructions for how to sign and return it. Once we receive it, we'll be able to +accept your pull requests. diff --git a/EclipseCodeFormat.xml b/EclipseCodeFormat.xml new file mode 100644 index 0000000..1af7985 --- /dev/null +++ b/EclipseCodeFormat.xml @@ -0,0 +1,341 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/README.md b/README.md deleted file mode 100644 index 0a166ce..0000000 --- a/README.md +++ /dev/null @@ -1,2 +0,0 @@ -dataflow-java -============= diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..9959b41 --- /dev/null +++ b/README.rst @@ -0,0 +1,146 @@ +============== +dataflow-java |Build Status|_ |Build Coverage|_ +============== + +.. |Build Status| image:: http://img.shields.io/travis/googlegenomics/dataflow-java.svg?style=flat +.. _Build Status: https://travis-ci.org/googlegenomics/dataflow-java + +.. |Build Coverage| image:: http://img.shields.io/coveralls/googlegenomics/dataflow-java.svg?style=flat +.. _Build Coverage: https://coveralls.io/r/googlegenomics/dataflow-java?branch=master + + If you are ready to start coding, take a look at the information below. But if you are + looking for a task-oriented list (e.g., `How do I compute principal coordinate analysis + with Google Genomics? `_), + a better place to start is the `Google Genomics Cookbook `_ . + +Getting started +--------------- + +#. First git clone this repository. + +#. If you have not already done so, follow the Google Genomics `getting started instructions `_ to set up your environment including `installing gcloud `_ and running ``gcloud init``. + +#. If you have not already done so, follow the Google Cloud Dataflow `getting started instructions `_ to set up your environment for Dataflow. + +#. This project now includes code for calling the Genomics API using `gRPC `_. To use gRPC, you'll need a version of ALPN that matches your JRE version. + + #. See the `ALPN documentation `_ for a table of which ALPN jar to use for your JRE version. + #. Then download the correct version from `here `_. + +Local Run +--------- +To use this code, build the client using `Apache Maven`_:: + + cd dataflow-java + mvn package + +Then you can run a pipeline locally with the command line, passing in the Project ID and Google Cloud Storage bucket you made in the first step. This command runs the VariantSimilarity pipeline (which runs PCoA on a dataset):: + + java -Xbootclasspath/p:/YOUR/PATH/TO/alpn-boot-YOUR-VERSION.jar \ + -cp target/google-genomics-dataflow*-runnable.jar \ + com.google.cloud.genomics.dataflow.pipelines.VariantSimilarity \ + --variantSetId=3049512673186936334 \ + --references=chr17:41196311:41277499 \ + --output=gs://your-bucket/output/localtest.txt + +Run on Google Compute Engine +---------------------------- +To deploy your pipeline (which runs on Google Compute Engine), ALPN is no longer needed but some additional command line arguments are required:: + + java -cp target/google-genomics-dataflow*-runnable.jar \ + com.google.cloud.genomics.dataflow.pipelines.VariantSimilarity \ + --project=your-project-id \ + --variantSetId=3049512673186936334 \ + --references=chr17:41196311:41277499 \ + --output=gs://your-bucket/output/test.txt \ + --runner=BlockingDataflowPipelineRunner \ + --project=your-project-id \ + --stagingLocation=gs://your-bucket/staging \ + --numWorkers=1 + +**See the** `Google Genomics Cookbook `_ **for more sample command lines for the various pipelines.** + +.. _Apache Maven: http://maven.apache.org/download.cgi + +Command Line Options +-------------------- + +Use ``--help`` to get more information about the command line options. Change +the pipeline class name below to match the one you would like to run:: + + java -cp google-genomics-dataflow*-runnable.jar \ + com.google.cloud.genomics.dataflow.pipelines.VariantSimilarity --help + +Code layout +----------- + +The `Main code directory `_ +contains several useful utilities: + +coders: + includes ``Coder`` classes that are useful for Genomics pipelines. ``GenericJsonCoder`` + can be used with any of the Java client library classes (like ``Read``, ``Variant``, etc) + +functions: + contains common DoFns that can be reused as part of any pipeline. + ``OutputPCoAFile`` is an example of a complex ``PTransform`` that provides a useful common analysis. + +pipelines: + contains example pipelines which demonstrate how Google Cloud Dataflow can work with Google Genomics + + * ``VariantSimilarity`` runs a principal coordinates analysis over a dataset containing variants, and + writes a file of graph results that can be easily displayed by Google Sheets. + + * ``IdentityByState`` runs IBS over a dataset containing variants. See the `results/ibs `_ + directory for more information on how to use the pipeline's results. + + * and several others! + +readers: + contains functions that perform API calls to read data from the genomics API + +utils: + contains utilities for running dataflow workflows against the genomics API + + * ``DataflowWorkarounds`` + contains workarounds needed to use the Google Cloud Dataflow APIs. + + * ``GenomicsOptions.java`` and ``GenomicsDatasetOptions`` + extend these classes for your command line options to take advantage of common command + line functionality + + +Maven artifact +-------------- +This code is also deployed as Maven artifacts through Sonatype, including both a normal jar and a runnable jar containing all dependencies (a fat jar). The +`utils-java readme `_ +has detailed instructions on how to deploy new versions. + +To depend on this code, add the following to your ``pom.xml`` file:: + + + + + com.google.cloud.genomics + google-genomics-dataflow + LATEST + + + + +You can find the latest version in +`Maven's central repository `_ + +For an example pipeline that depends on this code in another GitHub repository, see https://github.com/googlegenomics/codelabs/tree/master/Java/PlatinumGenomes-variant-transformation. + +Project status +-------------- + +Goals +~~~~~ +* Provide a Maven artifact which makes it easier to use Google Genomics within Google Cloud Dataflow. +* Provide some example pipelines which demonstrate how Dataflow can be used to analyze Genomics data. + +Current status +~~~~~~~~~~~~~~ +This code is in active development. See the github issues for more detail. diff --git a/lib/alpn-boot-7.1.3.v20150130.jar b/lib/alpn-boot-7.1.3.v20150130.jar new file mode 100644 index 0000000..b754518 Binary files /dev/null and b/lib/alpn-boot-7.1.3.v20150130.jar differ diff --git a/lib/alpn-boot-8.1.3.v20150130.jar b/lib/alpn-boot-8.1.3.v20150130.jar new file mode 100644 index 0000000..624b03b Binary files /dev/null and b/lib/alpn-boot-8.1.3.v20150130.jar differ diff --git a/pom.xml b/pom.xml new file mode 100644 index 0000000..68e3abf --- /dev/null +++ b/pom.xml @@ -0,0 +1,361 @@ + + + 4.0.0 + + Google Genomics and Dataflow + Google Genomics Dataflow pipelines. + https://github.com/googlegenomics/dataflow-java + com.google.cloud.genomics + google-genomics-dataflow + jar + v1beta2-0.18-SNAPSHOT + + + Google + http://www.google.com/ + + + + + The Apache Software License, Version 2.0 + http://www.apache.org/licenses/LICENSE-2.0.txt + repo + + + + + + cassiedoll + Cassie Doll + Google + http://www.google.com + -7 + + + kwestbrooks + Google + http://www.google.com + -7 + + + xzhangpeijin + Peijin Zhang + Google + http://www.google.com + -7 + + + + + scm:git:git@github.com:googlegenomics/dataflow-java.git + scm:git:git@github.com:googlegenomics/dataflow-java.git + git@github.com:googlegenomics/dataflow-java.git + HEAD + + + + + ossrh + https://oss.sonatype.org/content/repositories/snapshots/ + + + ossrh + https://oss.sonatype.org/service/local/staging/deploy/maven2/ + + + + + + + com.google.cloud.dataflow + google-cloud-dataflow-java-sdk-all + 1.3.0 + + + + + com.google.api-client + google-api-client + ${google.api.version} + + + + com.google.guava + guava-jdk5 + + + + + com.google.oauth-client + google-oauth-client + ${google.api.version} + + + com.google.oauth-client + google-oauth-client-jetty + ${google.api.version} + + + com.google.oauth-client + google-oauth-client-java6 + ${google.api.version} + + + com.google.http-client + google-http-client + ${google.api.version} + + + com.google.http-client + google-http-client-jackson2 + ${google.api.version} + + + com.google.apis + google-api-services-genomics + v1beta2-rev87-1.20.0 + + + + com.google.guava + guava-jdk5 + + + + + com.google.cloud.genomics + google-genomics-utils + v1beta2-0.38 + + + + com.google.guava + guava-jdk5 + + + + + + com.google.guava + guava + 18.0 + + + gov.nist.math.jama + gov.nist.math.jama + 1.1.1 + + + org.apache.commons + commons-math3 + 3.2 + + + org.reflections + reflections + 0.9.9 + + + junit + junit + 4.11 + test + + + org.hamcrest + hamcrest-all + 1.3 + test + + + org.mortbay.jetty + jetty + ${jetty.version} + runtime + + + org.mortbay.jetty + jetty-util + ${jetty.version} + runtime + + + javax.servlet + servlet-api + 2.5 + runtime + + + com.github.samtools + htsjdk + 1.128 + + + org.testng + testng + + + + + com.google.cloud.genomics + gatk-tools-java + 1.0 + + + com.google.protobuf + protobuf-java + 3.0.0-beta-1 + + + + + + release + + + + org.apache.maven.plugins + maven-gpg-plugin + 1.5 + + + sign-artifacts + verify + + sign + + + + + + + + + java7profile + + [1.7, 1.8) + + + ${basedir}/lib/alpn-boot-7.1.3.v20150130.jar + + + + java8profile + + [1.8, 1.9) + + + ${basedir}/lib/alpn-boot-8.1.3.v20150130.jar + + + + + + + + org.apache.maven.plugins + maven-compiler-plugin + 3.2 + + ${java.version} + ${java.version} + + + + + org.apache.maven.plugins + maven-release-plugin + 2.5 + + true + release + deploy + + + + + org.eluder.coveralls + coveralls-maven-plugin + 2.2.0 + + + + org.apache.maven.plugins + maven-shade-plugin + 2.3 + + + package + + shade + + + true + runnable + + + + + + + org.apache.maven.plugins + maven-dependency-plugin + 2.8 + + + copy-dependencies + package + + copy-dependencies + + + + + + + + org.apache.maven.plugins + maven-failsafe-plugin + 2.18.1 + + false + -Xbootclasspath/p:${alpn.jar} + + + + + integration-test + verify + + + + + + + + org.apache.maven.plugins + maven-jar-plugin + 2.6 + + + + + + + 1.7 + 6.1.26 + 4.11 + 1.19.0 + 2.4.2 + [1.7,) + UTF-8 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0.0329619 0.0354825 0.0343881 0.0336416 0.035523 0.0338642 0.0347381 0.0359862 0.0345783 0.0359033 0.035349 0.034997 0.0353733 0.034995 0.0342101 0.0349363 0.0348837 0.0365142 0.0362654 0.0352317 0.0357172 0.0348433 0.0341898 0.0339754 0.0350233 0.0354178 0.0363301 0.0345863 0.0346733 0.0344872 0.0353713 0.0375581 0.0365466 0.0353854 0.0353773 0.0356929 0.0362411 0.0378999 0.0374428 0.0353975 0.0361784 0.0337408 0.0359498 0.035264 0.0354077 0.0363423 0.0362128 0.0356727 0.0357374 0.0343274 0.0347644 0.0338358 0.0344832 0.0352135 0.0369815 0.0366012 0.0361865 0.0360449 0.035612 0.0350011 0.0359053 0.0358831 0.0362775 0.0344751 0.0356443 0.035086 0.0350678 0.0365891 0.0343476 0.0352802 0.034376 0.034643 0.0363059 0.0354016 0.0343719 0.0362654 0.0350961 0.036051 0.0361501 0.0352822 0.0342141 0.0344023 0.0351022 0.0358608 0.0364454 0.0340341 0.03456 0.035173 0.0372627 0.0356423 0.035705 0.0348615 0.0359255 0.0341838 0.0373376 0.0378959 0.0410294 0.0393706 0.0366781 0.0409425 0.0369815 0.0381751 0.0362674 0.0384866 0.037198 0.0370361 0.037109 0.0401029 0.037113 0.0356181 0.0411427 0.033943 0.0376289 0.0432547 0.038699 0.036672 0.0346572 0.0351872 0.034202 0.0380678 0.0382236 0.0368703 0.036227 0.0384805 0.0340442 0.0398804 0.0375662 0.0400645 0.0391238 0.0372951 0.0322235 0.0382094 0.0373517 0.0360004 0.0341049 0.037995 0.0400807 0.0369229 0.0394394 0.0389478 0.0350739 0.0375237 0.0379869 0.0380233 0.0390287 0.0392816 0.0354724 0.0384138 0.0385271 0.033939 0.0358082 0.0362229 0.0373699 0.0353551 0.0387233 0.0390834 0.037287 0.0349505 0.0395082 0.0371899 0.0402587 0.0382175 0.0361885 0.0346288 0.0389357 0.0363139 0.0351811 0.0406653 0.0387779 0.0374306 0.0356747 0.0357677 0.0378655 0.037726 0.0357152 0.0383126 0.0342991 0.036405 0.0346531 0.0357779 0.0352236 0.0344973 0.0354825 0.0380355 0.0360793 0.0393443 0.0375115 0.0364353 0.0370382 0.0397793 0.0367266 0.0390712 0.0392836 0.0346106 0.0417132 0.0343294 0.0404913 0.0340867 0.0398602 0.0379849 0.0350354 0.0372324 0.0376046 0.037819 0.0380031 0.0366214 0.0383713 0.0367752 0.0348433 0.0348716 0.0398238 0.0386019 0.0356646 0.0382985 0.0344751 0.0376774 0.0357475 0.037287 0.0347178 0.0374245 0.0378777 0.0384825 0.0418993 0.0388831 0.0376956 0.0391299 0.0380739 0.0402971 0.0388062 0.0401211 0.0415837 0.0384623 0.0384057 0.0366558 0.035703 0.0395871 0.039761 0.0407462 0.0403983 0.0412277 0.0381002 0.0402648 0.0407948 0.0398197 0.0397408 0.0390955 0.0395527 0.0416707 0.0386525 0.03949 0.0397914 0.036939 0.0385877 0.0394556 0.0411508 0.0391845 0.0425952 0.0379525 0.0403376 0.0410578 0.0392634 0.0380719 0.0400584 0.0378676 0.0394434 0.0394394 0.0411407 0.0398683 0.0387496 0.0377684 0.0382115 0.0404266 0.0381811 0.0395163 0.0394495 0.0401737 0.039138 0.0400787 0.038432 0.0404266 0.0416383 0.0416545 0.0406188 0.0380233 0.0403376 0.0390449 0.0377887 0.0373902 0.040198 0.0439688 0.0367448 0.0397449 0.0376329 0.0384704 0.0385837 0.0416181 0.0380132 0.0418629 0.0385008 0.0385169 0.0389883 0.037906 0.0417617 0.0408373 0.0398399 0.0394354 0.0395001 0.0380557 0.0392412 0.0405945 0.0387455 0.0401758 0.0367489 0.0378352 0.0394434 0.0419721 0.0389721 0.0391542 0.0385695 1 diff --git a/results/ibs/1000Genomes-chr22/analyze-ibs-data.Rmd b/results/ibs/1000Genomes-chr22/analyze-ibs-data.Rmd new file mode 100644 index 0000000..f58ed8f --- /dev/null +++ b/results/ibs/1000Genomes-chr22/analyze-ibs-data.Rmd @@ -0,0 +1,232 @@ + + + + + + + + + + + + + + +# Identity By State (IBS) for 1000 Genomes Chromosome 22 + +The following example makes use of [1000 +Genomes](https://cloud.google.com/genomics/data/1000-genomes). For more detail +about how this data was loaded into the Google Genomics API, please see [Google +Genomics Public Data](https://cloud.google.com/genomics/data/1000-genomes). + +```{r echo=FALSE, eval=FALSE} +# This codelab assumes that the current working directory is where the Rmd file +# resides +setwd("/YOUR/PATH/TO/1000Genomes-chr22/ibs") +``` + +## Computing IBS + +Follow the instructions at [README.rst](../../../README.rst) to compute the +Identity By State (IBS) scores for chr 22 of the [1000 Genomes data +set](https://cloud.google.com/genomics/data/1000-genomes). Specifically, first +configure and run the IBS DataFlow pipeline: + +```sh + java -cp ../../../target/google-genomics-dataflow-v1beta2-0.2-SNAPSHOT.jar \ + com.google.cloud.genomics.dataflow.pipelines.IdentityByState \ + --runner=BlockingDataflowPipelineRunner \ + --project=my-project-id \ + --stagingLocation=gs://my-bucket/staging \ + --output=gs://my-bucket/output/ibs.tsv \ + --numWorkers=40 \ + --references=22:16050407:51243297 +``` + +We used the following BigQuery command to compute the reference bounds in the +above command: + +```sql +SELECT + MIN(start) AS start, + MAX(end) AS end +FROM + [genomics-public-data:1000_genomes.variants] +WHERE + reference_name IN ("22") + ``` + +Next, merge the generated +[`1000genomes_chr22_ibs.tsv`](1000genomes_chr22_ibs.tsv) shards into a single +file: + +```sh + gsutil cat gs://my-bucket/output/is.tsv* | sort > 1000genomes_chr22_ibs.tsv +``` + +Finally, run [`generate.R`](generate.R) to visualize +[`1000genomes_chr22_ibs.tsv`](1000genomes_chr22_ibs.tsv) and compare it with +[the IBS scores computed by +PLINK/SEQ](https://raw.githubusercontent.com/googlegenomics/codelabs/master/R/1000Genomes-BRCA1-analysis/data/plinkseqIBS/chr22/ALL.chr22.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.ibs). + +## Loading IBS Data in R + +`ibsDataFlowFilename` contains an N^2 x 3 IBS matrix, where N is the size of the +population and each row represents the IBS score for a pair of individuals. + +```{r message=FALSE, comment=NA} +ibsDataFlowFilename="1000genomes_chr22_ibs.tsv" +``` + +`ibsPlinkSeqFilename` contains an NxN IBS matrix, where N is the size of the population +and each cell of the matrix contains the IBS score of a pair of individuals. + +```{r message=FALSE, comment=NA} +ibsPlinkSeqFilename="1000genomes_phase1_chr22_plinkseq_ibs.tsv" +``` + +```{r message=FALSE, comment=NA} +require(reshape2) +require(dplyr) + +ReadIBSFile <- function(ibsFilename, header=FALSE, rowNames=NULL) { + ibsData <- read.table(file=ibsFilename, header=header, + row.names=rowNames, stringsAsFactors=FALSE) + return (ibsData) +} +ibsDataflowData <- ReadIBSFile(ibsDataFlowFilename) +ibsPlinkSeqData <- ReadIBSFile(ibsPlinkSeqFilename, header=TRUE, rowNames=1) +``` + +Transform the NxN matrix into a N^2 x 3 matrix, where each row represents the +IBS score for a pair of individuals. + +```{r message=FALSE, comment=NA} +ibsPlinkSeqData <- melt(data.matrix(ibsPlinkSeqData)) +``` + +Set the column names of the two sets of IBS data consistently. + +```{r message=FALSE, comment=NA} +ColumnNames <- function(ibsData) { + if(3 == ncol(ibsData)) { + colnames(ibsData) <- c("sample1", "sample2", "ibsScore") + } else { + colnames(ibsData) <- c("sample1", "sample2", "ibsScore", "similar", "observed") + } +} +colnames(ibsDataflowData) <- ColumnNames(ibsDataflowData) +colnames(ibsPlinkSeqData) <- ColumnNames(ibsPlinkSeqData) +``` + +Make the IBS matrix symmetric. + +```{r message=FALSE, comment=NA} +MakeIBSDataSymmetric <- function(ibsData) { + ibsPairsMirrored <- data.frame(sample1=ibsData$sample2, + sample2=ibsData$sample1, + ibsScore=ibsData$ibsScore) + ibsData <- rbind(ibsData[,1:3], ibsPairsMirrored) +} +ibsDataflowData <- MakeIBSDataSymmetric(ibsDataflowData) +``` + +## IBS Heat Map + +Exclude the IBS values for a genome and itself, because those values are always +1.0 and skew the heat map. + +```{r message=FALSE, comment=NA} +ExcludeDiagonal <- function(ibsData) { + ibsData <- filter(ibsData, ibsData$sample1 != ibsData$sample2) + return (ibsData) +} +ibsPlinkSeqDataSample <- ExcludeDiagonal(ibsPlinkSeqData) +``` + +Extract the IBS matrix for a random sample of the individuals. + +```{r message=FALSE, comment=NA} +SampleIBSMatrix <- function(ibsData, sampleSize=50) { + individuals <- unique(ibsData$sample1) + sample <- sample(individuals, sampleSize) + ibsData <- subset(ibsData, ibsData$sample1 %in% sample) + ibsData <- subset(ibsData, ibsData$sample2 %in% sample) + return (ibsData) +} +ibsPlinkSeqDataSample <- SampleIBSMatrix(ibsPlinkSeqDataSample) +``` + +Draw a heat map based on the sampled IBS scores. + +```{r ibs-heat-map, fig.align="center", fig.width=10, fig.height=10, message=FALSE, comment=NA} +require(ggplot2) +DrawHeatMap <- function(ibsData) { + p <- ggplot(data=ibsData, aes(x=sample1, y=sample2)) + + theme(axis.ticks=element_blank(), axis.text=element_blank()) + + geom_tile(aes(fill=ibsScore), colour="white") + + scale_fill_gradient(low="white", high="steelblue", na.value="black", + guide=guide_colourbar(title= "IBS Score")) + + labs(list(title="Identity By State (IBS) Heat Map", + x="Sample", y="Sample")) + p +} +DrawHeatMap(ibsPlinkSeqDataSample) +``` + +## Comparison with [PLINK/SEQ](https://atgu.mgh.harvard.edu/plinkseq/) IBS + +Compare the IBS matrix generated by DataFlow with [the one generated by +PLINK/SEQ](https://raw.githubusercontent.com/deflaux/codelabs/qc-codelab/R/1000Genomes-BRCA1-analysis/data/plinkseqIBS/chr22/ALL.chr22.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.ibs) +and report the number of differences. + +```{r message=FALSE, comment=NA} +mergedIBS <- inner_join(ExcludeDiagonal(ibsDataflowData), + ExcludeDiagonal(ibsPlinkSeqData), + by = c(colnames(ibsDataflowData)[1:2])) +mergedDiffIBS <- mutate(mergedIBS, + almostEqualIBS = abs(mergedIBS$ibsScore.x - mergedIBS$ibsScore.y) < 1e-5) +nrow(mergedDiffIBS[mergedDiffIBS$almostEqualIBS == FALSE,]) +``` + +Plot the two IBS matrices to show their linear relationship. + +```{r ibs-lm, fig.align="center", fig.width=5, fig.height=5, message=FALSE, comment=NA} +ggplot(mergedIBS, aes(x=ibsScore.x, y=ibsScore.y)) + geom_point() +``` + +```{r message=FALSE, comment=NA} +model <- lm(ibsScore.y ~ ibsScore.x, mergedIBS) +summary(model) +``` + +Comparison of IBS Results to Pedigree +=================================================== + +First we fetch the pedigree information from the 1,000 Genomes project. +```{r message=FALSE, comment=NA} +pedigree <- read.delim("ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130606_sample_info/20130606_g1k.ped", as.is=TRUE) +summary(pedigree) +``` + +We add the population and family identifiers to each individual in our pair. +```{r message=FALSE, comment=NA} +ibs_sample1_ped <- inner_join(ExcludeDiagonal(ibsDataflowData), + select(pedigree, Individual.ID, Family.ID, Population), + by=c("sample1" = "Individual.ID")) +ibs_both_ped <- inner_join(ibs_sample1_ped, + select(pedigree, Individual.ID, Family.ID, Population), + by=c("sample2" = "Individual.ID")) +ibs_relationship <- mutate(ibs_both_ped, + relationship=ifelse(Family.ID.x == Family.ID.y, + "Same Family", + ifelse(Population.x == Population.y, + "Same Population", + "None"))) +``` + +And plot the scores for pairs by their relationship type: +```{r ibs-boxplot, fig.align="center", fig.width=10, fig.height=10, message=FALSE, comment=NA} +boxplot(ibsScore~relationship, data=ibs_relationship, main="Identity By State Results compared to Pedigree", + xlab="Relationship Type Between the Pair of Individuals", ylab="Identity By State Score") +``` diff --git a/results/ibs/1000Genomes-chr22/analyze-ibs-data.md b/results/ibs/1000Genomes-chr22/analyze-ibs-data.md new file mode 100644 index 0000000..c0f9ae5 --- /dev/null +++ b/results/ibs/1000Genomes-chr22/analyze-ibs-data.md @@ -0,0 +1,305 @@ + + + + + + + + + + + + + + +# Identity By State (IBS) for 1000 Genomes Chromosome 22 + +The following example makes use of [1000 +Genomes](https://cloud.google.com/genomics/data/1000-genomes). For more detail +about how this data was loaded into the Google Genomics API, please see [Google +Genomics Public Data](https://cloud.google.com/genomics/data/1000-genomes). + + + +## Computing IBS + +Follow the instructions at [README.rst](../../../README.rst) to compute the +Identity By State (IBS) scores for chr 22 of the [1000 Genomes data +set](https://cloud.google.com/genomics/data/1000-genomes). Specifically, first +configure and run the IBS DataFlow pipeline: + +```sh + java -cp ../../../target/google-genomics-dataflow-v1beta2-0.2-SNAPSHOT.jar \ + com.google.cloud.genomics.dataflow.pipelines.IdentityByState \ + --runner=BlockingDataflowPipelineRunner \ + --project=my-project-id \ + --stagingLocation=gs://my-bucket/staging \ + --output=gs://my-bucket/output/ibs.tsv \ + --numWorkers=40 \ + --references=22:16050407:51243297 +``` + +We used the following BigQuery command to compute the reference bounds in the +above command: + +```sql +SELECT + MIN(start) AS start, + MAX(end) AS end +FROM + [genomics-public-data:1000_genomes.variants] +WHERE + reference_name IN ("22") + ``` + +Next, merge the generated +[`1000genomes_chr22_ibs.tsv`](1000genomes_chr22_ibs.tsv) shards into a single +file: + +```sh + gsutil cat gs://my-bucket/output/is.tsv* | sort > 1000genomes_chr22_ibs.tsv +``` + +Finally, run [`generate.R`](generate.R) to visualize +[`1000genomes_chr22_ibs.tsv`](1000genomes_chr22_ibs.tsv) and compare it with +[the IBS scores computed by +PLINK/SEQ](https://raw.githubusercontent.com/googlegenomics/codelabs/master/R/1000Genomes-BRCA1-analysis/data/plinkseqIBS/chr22/ALL.chr22.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.ibs). + +## Loading IBS Data in R + +`ibsDataFlowFilename` contains an N^2 x 3 IBS matrix, where N is the size of the +population and each row represents the IBS score for a pair of individuals. + + +```r +ibsDataFlowFilename="1000genomes_chr22_ibs.tsv" +``` + +`ibsPlinkSeqFilename` contains an NxN IBS matrix, where N is the size of the population +and each cell of the matrix contains the IBS score of a pair of individuals. + + +```r +ibsPlinkSeqFilename="1000genomes_phase1_chr22_plinkseq_ibs.tsv" +``` + + +```r +require(reshape2) +require(dplyr) + +ReadIBSFile <- function(ibsFilename, header=FALSE, rowNames=NULL) { + ibsData <- read.table(file=ibsFilename, header=header, + row.names=rowNames, stringsAsFactors=FALSE) + return (ibsData) +} +ibsDataflowData <- ReadIBSFile(ibsDataFlowFilename) +ibsPlinkSeqData <- ReadIBSFile(ibsPlinkSeqFilename, header=TRUE, rowNames=1) +``` + +Transform the NxN matrix into a N^2 x 3 matrix, where each row represents the +IBS score for a pair of individuals. + + +```r +ibsPlinkSeqData <- melt(data.matrix(ibsPlinkSeqData)) +``` + +Set the column names of the two sets of IBS data consistently. + + +```r +ColumnNames <- function(ibsData) { + if(3 == ncol(ibsData)) { + colnames(ibsData) <- c("sample1", "sample2", "ibsScore") + } else { + colnames(ibsData) <- c("sample1", "sample2", "ibsScore", "similar", "observed") + } +} +colnames(ibsDataflowData) <- ColumnNames(ibsDataflowData) +colnames(ibsPlinkSeqData) <- ColumnNames(ibsPlinkSeqData) +``` + +Make the IBS matrix symmetric. + + +```r +MakeIBSDataSymmetric <- function(ibsData) { + ibsPairsMirrored <- data.frame(sample1=ibsData$sample2, + sample2=ibsData$sample1, + ibsScore=ibsData$ibsScore) + ibsData <- rbind(ibsData[,1:3], ibsPairsMirrored) +} +ibsDataflowData <- MakeIBSDataSymmetric(ibsDataflowData) +``` + +## IBS Heat Map + +Exclude the IBS values for a genome and itself, because those values are always +1.0 and skew the heat map. + + +```r +ExcludeDiagonal <- function(ibsData) { + ibsData <- filter(ibsData, ibsData$sample1 != ibsData$sample2) + return (ibsData) +} +ibsPlinkSeqDataSample <- ExcludeDiagonal(ibsPlinkSeqData) +``` + +Extract the IBS matrix for a random sample of the individuals. + + +```r +SampleIBSMatrix <- function(ibsData, sampleSize=50) { + individuals <- unique(ibsData$sample1) + sample <- sample(individuals, sampleSize) + ibsData <- subset(ibsData, ibsData$sample1 %in% sample) + ibsData <- subset(ibsData, ibsData$sample2 %in% sample) + return (ibsData) +} +ibsPlinkSeqDataSample <- SampleIBSMatrix(ibsPlinkSeqDataSample) +``` + +Draw a heat map based on the sampled IBS scores. + + +```r +require(ggplot2) +DrawHeatMap <- function(ibsData) { + p <- ggplot(data=ibsData, aes(x=sample1, y=sample2)) + + theme(axis.ticks=element_blank(), axis.text=element_blank()) + + geom_tile(aes(fill=ibsScore), colour="white") + + scale_fill_gradient(low="white", high="steelblue", na.value="black", + guide=guide_colourbar(title= "IBS Score")) + + labs(list(title="Identity By State (IBS) Heat Map", + x="Sample", y="Sample")) + p +} +DrawHeatMap(ibsPlinkSeqDataSample) +``` + +plot of chunk ibs-heat-map + +## Comparison with [PLINK/SEQ](https://atgu.mgh.harvard.edu/plinkseq/) IBS + +Compare the IBS matrix generated by DataFlow with [the one generated by +PLINK/SEQ](https://raw.githubusercontent.com/deflaux/codelabs/qc-codelab/R/1000Genomes-BRCA1-analysis/data/plinkseqIBS/chr22/ALL.chr22.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.ibs) +and report the number of differences. + + +```r +mergedIBS <- inner_join(ExcludeDiagonal(ibsDataflowData), + ExcludeDiagonal(ibsPlinkSeqData), + by = c(colnames(ibsDataflowData)[1:2])) +mergedDiffIBS <- mutate(mergedIBS, + almostEqualIBS = abs(mergedIBS$ibsScore.x - mergedIBS$ibsScore.y) < 1e-5) +nrow(mergedDiffIBS[mergedDiffIBS$almostEqualIBS == FALSE,]) +``` + +``` +[1] 1032 +``` + +Plot the two IBS matrices to show their linear relationship. + + +```r +ggplot(mergedIBS, aes(x=ibsScore.x, y=ibsScore.y)) + geom_point() +``` + +plot of chunk ibs-lm + + +```r +model <- lm(ibsScore.y ~ ibsScore.x, mergedIBS) +summary(model) +``` + +``` + +Call: +lm(formula = ibsScore.y ~ ibsScore.x, data = mergedIBS) + +Residuals: + Min 1Q Median 3Q Max +-1.908e-05 -9.064e-07 -8.521e-07 1.116e-06 1.207e-06 + +Coefficients: + Estimate Std. Error t value Pr(>|t|) +(Intercept) -1.266e-06 8.181e-09 -154.8 <2e-16 *** +ibsScore.x 1.000e+00 2.279e-07 4388578.9 <2e-16 *** +--- +Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 + +Residual standard error: 1.136e-06 on 1191370 degrees of freedom +Multiple R-squared: 1, Adjusted R-squared: 1 +F-statistic: 1.926e+13 on 1 and 1191370 DF, p-value: < 2.2e-16 +``` + +Comparison of IBS Results to Pedigree +=================================================== + +First we fetch the pedigree information from the 1,000 Genomes project. + +```r +pedigree <- read.delim("ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130606_sample_info/20130606_g1k.ped", as.is=TRUE) +summary(pedigree) +``` + +``` + Family.ID Individual.ID Paternal.ID + Length:3501 Length:3501 Length:3501 + Class :character Class :character Class :character + Mode :character Mode :character Mode :character + + + + Maternal.ID Gender Phenotype Population + Length:3501 Min. :1.000 Min. :0 Length:3501 + Class :character 1st Qu.:1.000 1st Qu.:0 Class :character + Mode :character Median :2.000 Median :0 Mode :character + Mean :1.503 Mean :0 + 3rd Qu.:2.000 3rd Qu.:0 + Max. :2.000 Max. :0 + Relationship Siblings Second.Order + Length:3501 Length:3501 Length:3501 + Class :character Class :character Class :character + Mode :character Mode :character Mode :character + + + + Third.Order Other.Comments + Length:3501 Length:3501 + Class :character Class :character + Mode :character Mode :character + + + +``` + +We add the population and family identifiers to each individual in our pair. + +```r +ibs_sample1_ped <- inner_join(ExcludeDiagonal(ibsDataflowData), + select(pedigree, Individual.ID, Family.ID, Population), + by=c("sample1" = "Individual.ID")) +ibs_both_ped <- inner_join(ibs_sample1_ped, + select(pedigree, Individual.ID, Family.ID, Population), + by=c("sample2" = "Individual.ID")) +ibs_relationship <- mutate(ibs_both_ped, + relationship=ifelse(Family.ID.x == Family.ID.y, + "Same Family", + ifelse(Population.x == Population.y, + "Same Population", + "None"))) +``` + +And plot the scores for pairs by their relationship type: + +```r +boxplot(ibsScore~relationship, data=ibs_relationship, main="Identity By State Results compared to Pedigree", + xlab="Relationship Type Between the Pair of Individuals", ylab="Identity By State Score") +``` + +plot of chunk ibs-boxplot diff --git a/results/ibs/1000Genomes-chr22/figure/ibs-boxplot-1.png b/results/ibs/1000Genomes-chr22/figure/ibs-boxplot-1.png new file mode 100644 index 0000000..e7aa52c Binary files /dev/null and b/results/ibs/1000Genomes-chr22/figure/ibs-boxplot-1.png differ diff --git a/results/ibs/1000Genomes-chr22/figure/ibs-heat-map-1.png b/results/ibs/1000Genomes-chr22/figure/ibs-heat-map-1.png new file mode 100644 index 0000000..b44581a Binary files /dev/null and b/results/ibs/1000Genomes-chr22/figure/ibs-heat-map-1.png differ diff --git a/results/ibs/1000Genomes-chr22/figure/ibs-lm-1.png b/results/ibs/1000Genomes-chr22/figure/ibs-lm-1.png new file mode 100644 index 0000000..076fa15 Binary files /dev/null and b/results/ibs/1000Genomes-chr22/figure/ibs-lm-1.png differ diff --git a/results/ibs/1000Genomes-chr22/generate.R b/results/ibs/1000Genomes-chr22/generate.R new file mode 100755 index 0000000..d345949 --- /dev/null +++ b/results/ibs/1000Genomes-chr22/generate.R @@ -0,0 +1,24 @@ +#!/usr/bin/env Rscript + +# Copyright 2014 Google Inc. All rights reserved. +# +# Licensed under the Apache License, Version 2.0 (the 'License'); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an 'AS IS' BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +library("rmarkdown") +library("knitr") + +rmdFile <- "analyze-ibs-data.Rmd" +purl(rmdFile, documentation=1) +knit(rmdFile) +render(rmdFile) + diff --git a/src/main/java/com/google/cloud/genomics/dataflow/coders/DelegatingAtomicCoder.java b/src/main/java/com/google/cloud/genomics/dataflow/coders/DelegatingAtomicCoder.java new file mode 100644 index 0000000..eaa664b --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/coders/DelegatingAtomicCoder.java @@ -0,0 +1,52 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.coders; + +import com.google.cloud.dataflow.sdk.coders.AtomicCoder; +import com.google.cloud.dataflow.sdk.coders.Coder; +import com.google.cloud.dataflow.sdk.coders.CoderException; +import com.google.cloud.dataflow.sdk.coders.Coder.NonDeterministicException; + +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; + +public abstract class DelegatingAtomicCoder extends AtomicCoder { + + private final Coder delegate; + + protected DelegatingAtomicCoder(Coder delegate) { + this.delegate = delegate; + } + + @Override public final X decode(InputStream inStream, Context context) + throws CoderException, IOException { + return from(delegate.decode(inStream, context)); + } + + @Override public final void encode(X value, OutputStream outStream, Context context) + throws CoderException, IOException { + delegate.encode(to(value), outStream, context); + } + + protected abstract X from(Y object) throws CoderException, IOException; + + public void verifyDeterministic() throws NonDeterministicException { + delegate.verifyDeterministic(); + } + + protected abstract Y to(X object) throws CoderException, IOException; +} \ No newline at end of file diff --git a/src/main/java/com/google/cloud/genomics/dataflow/coders/DelegatingStandardCoder.java b/src/main/java/com/google/cloud/genomics/dataflow/coders/DelegatingStandardCoder.java new file mode 100644 index 0000000..bed171e --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/coders/DelegatingStandardCoder.java @@ -0,0 +1,57 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.coders; + +import com.google.cloud.dataflow.sdk.coders.Coder; +import com.google.cloud.dataflow.sdk.coders.CoderException; +import com.google.cloud.dataflow.sdk.coders.StandardCoder; + +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.util.List; + +public abstract class DelegatingStandardCoder extends StandardCoder { + + private final Coder delegate; + + protected DelegatingStandardCoder(Coder delegate) { + this.delegate = delegate; + } + + @Override + public List> getCoderArguments() { + return delegate.getCoderArguments(); + } + + @Override public final X decode(InputStream inStream, Context context) + throws CoderException, IOException { + return from(delegate.decode(inStream, context)); + } + + @Override public final void encode(X value, OutputStream outStream, Context context) + throws CoderException, IOException { + delegate.encode(to(value), outStream, context); + } + + protected abstract X from(Y object) throws CoderException, IOException; + + public void verifyDeterministic() throws NonDeterministicException { + delegate.verifyDeterministic(); + } + + protected abstract Y to(X object) throws CoderException, IOException; +} \ No newline at end of file diff --git a/src/main/java/com/google/cloud/genomics/dataflow/coders/GenericJsonCoder.java b/src/main/java/com/google/cloud/genomics/dataflow/coders/GenericJsonCoder.java new file mode 100644 index 0000000..a859020 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/coders/GenericJsonCoder.java @@ -0,0 +1,102 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.coders; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.google.api.client.googleapis.util.Utils; +import com.google.api.client.json.GenericJson; +import com.google.api.client.json.JsonFactory; +import com.google.cloud.dataflow.sdk.coders.CannotProvideCoderException; +import com.google.cloud.dataflow.sdk.coders.Coder; +import com.google.cloud.dataflow.sdk.coders.CoderProvider; +import com.google.cloud.dataflow.sdk.coders.Proto2Coder; +import com.google.cloud.dataflow.sdk.coders.SerializableCoder; +import com.google.cloud.dataflow.sdk.coders.StringUtf8Coder; +import com.google.cloud.dataflow.sdk.util.CloudObject; +import com.google.cloud.dataflow.sdk.values.TypeDescriptor; +import com.google.protobuf.Message; + +import java.io.IOException; +import java.io.Serializable; + +/** + * Can be used as a coder for any object that extends GenericJson. + * This includes all objects in the Google Genomics Java client library. +*/ +public class GenericJsonCoder extends DelegatingAtomicCoder { + + private static final JsonFactory JSON_FACTORY = Utils.getDefaultJsonFactory(); + private static final Coder STRING_CODER = StringUtf8Coder.of(); + + public static GenericJsonCoder of(Class type) { + return new GenericJsonCoder<>(type); + } + + @JsonCreator + @SuppressWarnings("unchecked") + public static GenericJsonCoder of(@JsonProperty("type") String type) + throws ClassNotFoundException { + return of((Class) Class.forName(type)); + } + + private final Class type; + + private GenericJsonCoder(Class type) { + super(STRING_CODER); + this.type = type; + } + + @Override + public CloudObject asCloudObject() { + CloudObject result = super.asCloudObject(); + result.put("type", type.getName()); + return result; + } + + @Override protected T from(String object) throws IOException { + return JSON_FACTORY.fromString(object, type); + } + + @Override protected String to(T object) throws IOException { + return JSON_FACTORY.toString(object); + } + + /** + * Coder provider for all objects in the Google Genomics Java client library. + */ + public static final CoderProvider PROVIDER = new CoderProvider() { + @Override + @SuppressWarnings("unchecked") + public Coder getCoder(TypeDescriptor typeDescriptor) + throws CannotProvideCoderException { + Class rawType = (Class) typeDescriptor.getRawType(); + if (!GenericJson.class.isAssignableFrom(rawType)) { + if (Message.class.isAssignableFrom(rawType)) { + return (Coder) Proto2Coder.of((Class) rawType); + } else if (Serializable.class.isAssignableFrom(rawType)) { + // Fall back this here because if this is used as the follback coder, it overwrites the + // default fallback CoderProvider of SerializableCoder.PROVIDER. + return (Coder) SerializableCoder.of((Class) rawType); + } else { + throw new CannotProvideCoderException("Class " + rawType + + " does not implement GenericJson, Message, or Serializable"); + } + } + return (Coder) GenericJsonCoder.of((Class) rawType); + } + }; +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/AlleleSimilarityCalculator.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/AlleleSimilarityCalculator.java new file mode 100644 index 0000000..1283c5f --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/AlleleSimilarityCalculator.java @@ -0,0 +1,107 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import java.util.HashMap; +import java.util.Map; + +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.genomics.dataflow.utils.CallFilters; +import com.google.cloud.genomics.dataflow.utils.PairGenerator; +import com.google.cloud.genomics.utils.grpc.VariantUtils; +import com.google.common.collect.ImmutableList; +import com.google.common.collect.Maps; +import com.google.genomics.v1.Variant; +import com.google.genomics.v1.VariantCall; + +/** + * For each pair of calls on any of the given variants, computes a score, a number between 0 and 1 + * (inclusive), which represents the degree of the similarity of the two calls. Then, it emits the + * sum and number of the computed scores for each pair of call set names across all the given + * variants. + */ +public class AlleleSimilarityCalculator extends + DoFn, KV>> { + + private CallSimilarityCalculatorFactory callSimilarityCalculatorFactory; + + // HashMap, + private HashMap, KV> accumulator; + // TODO consider using guava MultiSet instead + + public AlleleSimilarityCalculator(CallSimilarityCalculatorFactory callSimilarityCalculatorFactory) { + this.callSimilarityCalculatorFactory = callSimilarityCalculatorFactory; + } + + @Override + public void startBundle(Context c) { + accumulator = Maps.newHashMap(); + } + + @Override + public void processElement(ProcessContext context) { + Variant variant = context.element(); + CallSimilarityCalculator callSimilarityCalculator = + callSimilarityCalculatorFactory.get(isReferenceMajor(variant)); + for (KV pair : PairGenerator.WITHOUT_REPLACEMENT.allPairs( + getSamplesWithVariant(variant), VariantUtils.CALL_COMPARATOR)) { + accumulateCallSimilarity(callSimilarityCalculator, pair.getKey(), pair.getValue()); + } + } + + private void accumulateCallSimilarity(CallSimilarityCalculator callSimilarityCalculator, + VariantCall call1, VariantCall call2) { + KV callPair = KV.of(call1.getCallSetName(), call2.getCallSetName()); + KV callPairAccumulation = accumulator.get(callPair); + if (callPairAccumulation == null) { + callPairAccumulation = KV.of(0.0, 0); + accumulator.put(callPair, callPairAccumulation); + } + accumulator.put(callPair, KV.of( + callPairAccumulation.getKey() + callSimilarityCalculator.similarity(call1, call2), + callPairAccumulation.getValue() + 1)); + } + + @Override + public void finishBundle(Context context) { + output(context, accumulator); + } + + static ImmutableList getSamplesWithVariant(Variant variant) { + return CallFilters.getSamplesWithVariantOfMinGenotype(variant, 0); + } + + static boolean isReferenceMajor(Variant variant) { + int referenceAlleles = 0; + int alternateAlleles = 0; + for (VariantCall call : variant.getCallsList()) { + for (Integer i : call.getGenotypeList()) { + if (i == 0) { + ++referenceAlleles; + } else if (i > 0) { + ++alternateAlleles; + } + } + } + return referenceAlleles >= alternateAlleles; + } + + static void output(DoFn>.Context context, Map map) { + for (Map.Entry entry : map.entrySet()) { + context.output(KV.of(entry.getKey(), entry.getValue())); + } + } + +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/CalculateTransmissionProbability.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/CalculateTransmissionProbability.java new file mode 100644 index 0000000..7597a96 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/CalculateTransmissionProbability.java @@ -0,0 +1,46 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.genomics.dataflow.model.Allele; + +/* + * Calculates the Transmission probability of each Allele. + * + * For now, this class only calculates only a simple ratio by dividing the number of observed + * transmission of a certain allele (i.e. total times this allele is observed in a child) with the + * total number of occurences of the allele. + */ + +public class CalculateTransmissionProbability + extends DoFn>, KV> { + + @Override + public void processElement(ProcessContext c) { + KV> input = c.element(); + double transmitted = 0, total = 0; + for (Boolean b : input.getValue()) { + if (b) { + transmitted += 1; + } + total += 1; + } + double tp = transmitted / total; + c.output(KV.of(input.getKey(), tp)); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/CallSimilarityCalculator.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/CallSimilarityCalculator.java new file mode 100644 index 0000000..15d87fe --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/CallSimilarityCalculator.java @@ -0,0 +1,24 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import com.google.genomics.v1.VariantCall; + +public interface CallSimilarityCalculator { + + double similarity(VariantCall call1, VariantCall call2); + +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/CallSimilarityCalculatorFactory.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/CallSimilarityCalculatorFactory.java new file mode 100644 index 0000000..bc40819 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/CallSimilarityCalculatorFactory.java @@ -0,0 +1,28 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import java.io.Serializable; + +public interface CallSimilarityCalculatorFactory extends Serializable { + + /** + * @param isReferenceMajor is true if and only if the reference allele is the major allele. + * @return an object to compare the similarity of any pair of calls. + */ + public abstract CallSimilarityCalculator get(boolean isReferenceMajor); + +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/CombineShardsFn.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/CombineShardsFn.java new file mode 100644 index 0000000..54a6cfe --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/CombineShardsFn.java @@ -0,0 +1,211 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import com.google.api.services.storage.model.ComposeRequest; +import com.google.api.services.storage.model.ComposeRequest.SourceObjects; +import com.google.api.services.storage.model.StorageObject; +import com.google.api.services.storage.Storage; +import com.google.api.services.storage.Storage.Objects.Compose; + +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.util.GcsUtil; +import com.google.cloud.dataflow.sdk.util.gcsfs.GcsPath; +import com.google.cloud.dataflow.sdk.util.Transport; +import com.google.cloud.dataflow.sdk.values.PCollectionView; +import com.google.cloud.genomics.dataflow.readers.bam.BAMIO; +import com.google.cloud.genomics.dataflow.utils.GCSOptions; +import com.google.cloud.genomics.dataflow.utils.GCSOutputOptions; + +import com.google.common.base.Stopwatch; +import com.google.common.collect.Lists; + +import htsjdk.samtools.BAMIndexer; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SamReader; +import htsjdk.samtools.ValidationStringency; +import htsjdk.samtools.util.BlockCompressedStreamConstants; + +import java.io.IOException; +import java.io.OutputStream; +import java.nio.channels.Channels; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; +import java.util.concurrent.TimeUnit; +import java.util.logging.Logger; + +/* + * Takes a set of BAM files that have been written to disk, concatenates them into one + * file (removing unneeded EOF blocks), and writes an index for the combined file. + */ +public class CombineShardsFn extends DoFn { + + public static interface Options extends GCSOutputOptions, GCSOptions {} + + private static final int MAX_FILES_FOR_COMPOSE = 32; + private static final String BAM_INDEX_FILE_MIME_TYPE = "application/octet-stream"; + private static final Logger LOG = Logger.getLogger(CombineShardsFn.class.getName()); + + final PCollectionView> shards; + + public CombineShardsFn(PCollectionView> shards) { + this.shards = shards; + } + + @Override + public void processElement(DoFn.ProcessContext c) throws Exception { + final String result = + combineShards( + c.getPipelineOptions().as(Options.class), + c.element(), + c.sideInput(shards)); + c.output(result); + } + + static String combineShards(Options options, String dest, + Iterable shards) throws IOException { + LOG.info("Combining shards into " + dest); + final Storage.Objects storage = Transport.newStorageClient( + options + .as(GCSOptions.class)) + .build() + .objects(); + + ArrayList sortedShardsNames = Lists.newArrayList(shards); + Collections.sort(sortedShardsNames); + + // Write an EOF block (empty gzip block), and put it at the end. + String eofFileName = options.getOutput() + "-EOF"; + final OutputStream os = Channels.newOutputStream( + (new GcsUtil.GcsUtilFactory()).create(options).create( + GcsPath.fromUri(eofFileName), + BAM_INDEX_FILE_MIME_TYPE)); + os.write(BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK); + os.close(); + sortedShardsNames.add(eofFileName); + + int stageNumber = 0; + /* + * GCS Compose method takes only up to 32 files, so if we have more + * shards than that we need to do a hierarchical combine: + * first combine all original shards in groups no more than 32 + * and then collect the results of these combines and so on until + * we have a group of no more than 32 that we can finally combine into + * a single file. + */ + while (sortedShardsNames.size() > MAX_FILES_FOR_COMPOSE) { + LOG.info("Stage " + stageNumber + ": Have " + sortedShardsNames.size() + + " shards: must combine in groups of " + MAX_FILES_FOR_COMPOSE); + final ArrayList combinedShards = Lists.newArrayList(); + for (int idx = 0; idx < sortedShardsNames.size(); idx += MAX_FILES_FOR_COMPOSE) { + final int endIdx = Math.min(idx + MAX_FILES_FOR_COMPOSE, + sortedShardsNames.size()); + final List combinableShards = sortedShardsNames.subList( + idx, endIdx); + final String intermediateCombineResultName = dest + "-" + + String.format("%02d",stageNumber) + "-" + + String.format("%02d",idx) + "-" + + String.format("%02d",endIdx); + final String combineResult = composeAndCleanUpShards(storage, + combinableShards, intermediateCombineResultName); + combinedShards.add(combineResult); + LOG.info("Stage " + stageNumber + ": adding combine result for " + + idx + "-" + endIdx + ": " + combineResult); + } + LOG.info("Stage " + stageNumber + ": moving to next stage with " + + combinedShards.size() + "shards"); + sortedShardsNames = combinedShards; + stageNumber++; + } + + LOG.info("Combining a final group of " + sortedShardsNames.size() + " shards"); + final String combineResult = composeAndCleanUpShards(storage, + sortedShardsNames, dest); + generateIndex(options, storage, combineResult); + return combineResult; + } + + static void generateIndex(Options options, + Storage.Objects storage, String bamFilePath) throws IOException { + final String baiFilePath = bamFilePath + ".bai"; + Stopwatch timer = Stopwatch.createStarted(); + LOG.info("Generating BAM index: " + baiFilePath); + LOG.info("Reading BAM file: " + bamFilePath); + final SamReader reader = BAMIO.openBAM(storage, bamFilePath, ValidationStringency.LENIENT, true); + + final OutputStream outputStream = + Channels.newOutputStream( + new GcsUtil.GcsUtilFactory().create(options) + .create(GcsPath.fromUri(baiFilePath), + BAM_INDEX_FILE_MIME_TYPE)); + BAMIndexer indexer = new BAMIndexer(outputStream, reader.getFileHeader()); + + long processedReads = 0; + + // create and write the content + for (SAMRecord rec : reader) { + if (++processedReads % 1000000 == 0) { + dumpStats(processedReads, timer); + } + indexer.processAlignment(rec); + } + indexer.finish(); + dumpStats(processedReads, timer); + } + + static void dumpStats(long processedReads, Stopwatch timer) { + LOG.info("Processed " + processedReads + " records in " + timer + + ". Speed: " + processedReads/timer.elapsed(TimeUnit.SECONDS) + " reads/sec"); + + } + + static String composeAndCleanUpShards(Storage.Objects storage, + List shardNames, String dest) throws IOException { + LOG.info("Combining shards into " + dest); + + final GcsPath destPath = GcsPath.fromUri(dest); + + StorageObject destination = new StorageObject() + .setContentType(BAM_INDEX_FILE_MIME_TYPE); + + ArrayList sourceObjects = new ArrayList(); + int addedShardCount = 0; + for (String shard : shardNames) { + final GcsPath shardPath = GcsPath.fromUri(shard); + LOG.info("Adding shard " + shardPath + " for result " + dest); + sourceObjects.add( new SourceObjects().setName(shardPath.getObject())); + addedShardCount++; + } + LOG.info("Added " + addedShardCount + " shards for composition"); + + final ComposeRequest composeRequest = new ComposeRequest() + .setDestination(destination) + .setSourceObjects(sourceObjects); + final Compose compose = storage.compose( + destPath.getBucket(), destPath.getObject(), composeRequest); + final StorageObject result = compose.execute(); + final String combineResult = GcsPath.fromObject(result).toString(); + LOG.info("Combine result is " + combineResult); + for (SourceObjects sourceObject : sourceObjects) { + final String shardToDelete = sourceObject.getName(); + LOG.info("Cleaning up shard " + shardToDelete + " for result " + dest); + storage.delete(destPath.getBucket(), shardToDelete).execute(); + } + + return combineResult; + } +} \ No newline at end of file diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/ExtractAlleleTransmissionStatus.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/ExtractAlleleTransmissionStatus.java new file mode 100644 index 0000000..fd8f85b --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/ExtractAlleleTransmissionStatus.java @@ -0,0 +1,103 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import com.google.api.services.genomics.model.Call; +import com.google.api.services.genomics.model.Variant; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.genomics.dataflow.model.Allele; +import com.google.common.annotations.VisibleForTesting; +import com.google.common.collect.Lists; + +import java.util.List; + +/** + * Emits String, (Allele, Boolean) pairs for each Allele a parent has. + * The String is the Id of the Variant, and the Boolean is set to True + * if the child has the Allele, False if not. + * i.e. + * If the genotype of the family is: + * Mother: AC, Father TG, Child is AG, function emits: + * (A, True), (C, False), (T, False), (G, True) + */ +public class ExtractAlleleTransmissionStatus + extends DoFn> { + + private class Trio { + String mom, dad, child; + Trio(String m, String d, String c) { + mom = m; + dad = d; + child = c; + } + } + + List getTrios() { + // TODO(gunan): Replace this with actual fetching of family informtion. + List trioList = Lists.newArrayList(); + // All Trio's are ordered as "mom, dad and child". + trioList.add(new Trio("NA12889", "NA12890", "NA12877")); + trioList.add(new Trio("NA12891", "NA12892", "NA12878")); + trioList.add(new Trio("NA12877", "NA12878", "NA12879")); + trioList.add(new Trio("NA12877", "NA12878", "NA12880")); + trioList.add(new Trio("NA12877", "NA12878", "NA12881")); + trioList.add(new Trio("NA12877", "NA12878", "NA12882")); + trioList.add(new Trio("NA12877", "NA12878", "NA12883")); + trioList.add(new Trio("NA12877", "NA12878", "NA12884")); + trioList.add(new Trio("NA12877", "NA12878", "NA12885")); + trioList.add(new Trio("NA12877", "NA12878", "NA12886")); + trioList.add(new Trio("NA12877", "NA12878", "NA12887")); + trioList.add(new Trio("NA12877", "NA12878", "NA12888")); + trioList.add(new Trio("NA12877", "NA12878", "NA12893")); + return trioList; + } + + @Override + public void processElement(ProcessContext c) { + Variant variant = c.element(); + List trioList = getTrios(); + + List sequences = variant.getAlternateBases(); + sequences.add(0, variant.getReferenceBases()); + + for (Trio family : trioList) { + List childGenotypes = getSample(variant, family.child) + .getGenotype(); + + List parentGenotypes = Lists.newArrayList(); + parentGenotypes.addAll(getSample(variant, family.mom).getGenotype()); + parentGenotypes.addAll(getSample(variant, family.dad).getGenotype()); + + for (Integer i: parentGenotypes) { + c.output(KV.of(new Allele(variant.getId(), + variant.getStart(), + sequences.get(i)), + childGenotypes.contains(i))); + childGenotypes.remove(i); + } + } + } + + @VisibleForTesting + Call getSample(Variant variant, String sampleName) { + for (Call call : variant.getCalls()) { + if (call.getCallSetName() == sampleName) + return call; + } + return null; + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/ExtractSimilarCallsets.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/ExtractSimilarCallsets.java new file mode 100644 index 0000000..7e46c66 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/ExtractSimilarCallsets.java @@ -0,0 +1,97 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import com.google.api.services.genomics.model.Call; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.genomics.dataflow.utils.CallFilters; +import com.google.cloud.genomics.dataflow.utils.PairGenerator; +import com.google.common.base.Function; +import com.google.common.collect.BiMap; +import com.google.common.collect.FluentIterable; +import com.google.common.collect.ImmutableList; +import com.google.common.collect.ImmutableMultiset; +import com.google.common.collect.Iterables; +import com.google.common.collect.Multiset; +import com.google.common.collect.Ordering; +import com.google.genomics.v1.Variant; +import com.google.genomics.v1.VariantCall; + +/** + * Emits a callset pair every time they share a variant. + */ +public class ExtractSimilarCallsets { + + abstract static class ExtractSimilarCallsetsBase extends DoFn, Long>> { + + private ImmutableMultiset.Builder> accumulator; + + @Override + public void startBundle(Context c) { + accumulator = ImmutableMultiset.builder(); + } + + @Override + public void processElement(ProcessContext context) { + FluentIterable> pairs = PairGenerator.WITH_REPLACEMENT.allPairs( + getSamplesWithVariant(context.element()), Ordering.natural()); + for (KV pair : pairs) { + accumulator.add(pair); + } + } + + @Override + public void finishBundle(Context context) { + for (Multiset.Entry> entry : accumulator.build().entrySet()) { + context.output(KV.of(entry.getElement(), Long.valueOf(entry.getCount()))); + } + } + + protected abstract ImmutableList getSamplesWithVariant(V variant); + } + + public static class v1 extends ExtractSimilarCallsetsBase { + + @Override + protected ImmutableList getSamplesWithVariant(Variant variant) { + return ImmutableList.copyOf(Iterables.transform( + CallFilters.getSamplesWithVariantOfMinGenotype(variant, 1), new Function() { + + @Override + public String apply(VariantCall call) { + return call.getCallSetName(); + } + + })); + } + } + + @Deprecated // Remove this when fully migrated to gRPC. + public static class v1beta2 extends ExtractSimilarCallsetsBase { + + @Override + protected ImmutableList getSamplesWithVariant(com.google.api.services.genomics.model.Variant variant) { + return ImmutableList.copyOf(Iterables.transform( + CallFilters.getSamplesWithVariantOfMinGenotype(variant, 1), new Function() { + + @Override + public String apply(Call call) { + return call.getCallSetName(); + } + + })); + } + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/FormatIBSData.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/FormatIBSData.java new file mode 100644 index 0000000..0d28319 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/FormatIBSData.java @@ -0,0 +1,36 @@ +/* + * Copyright 2014 Google Inc. All rights reserved. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ + +package com.google.cloud.genomics.dataflow.functions; + +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.common.base.Joiner; + +/** + * Computes the IBS score based on the given sums of ratios and numbers of shared alleles. Then, it + * outputs the results to a file. + */ +public final class FormatIBSData extends DoFn, KV>, String> { + @Override + public void processElement(ProcessContext c) { + KV, KV> result = c.element(); + String call1 = result.getKey().getKey(); + String call2 = result.getKey().getValue(); + Double sumOfRatios = result.getValue().getKey(); + int numberOfRatios = result.getValue().getValue(); + c.output(Joiner.on('\t').join(call1, call2, sumOfRatios / numberOfRatios, sumOfRatios, + numberOfRatios)); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/IBSCalculator.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/IBSCalculator.java new file mode 100644 index 0000000..dd4db4e --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/IBSCalculator.java @@ -0,0 +1,41 @@ +/* +Copyright 2014 Google Inc. All rights reserved. + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. +*/ +package com.google.cloud.genomics.dataflow.functions; + +import com.google.cloud.dataflow.sdk.transforms.SerializableFunction; +import com.google.cloud.dataflow.sdk.values.KV; + +/** + * Sums up a number of pairs of a double and an int to a single pair. + * + * Each pair represents the sum of ratio and number of shared alleles between two call set names for + * a set of variants. + */ +public final class IBSCalculator implements + SerializableFunction>, KV> { + + @Override + public KV apply(Iterable> sharedAllelesInfos) { + double sumOfRatios = 0.0; + int numberOfRatios = 0; + for (KV info : sharedAllelesInfos) { + sumOfRatios += info.getKey(); + numberOfRatios += info.getValue(); + } + return KV.of(sumOfRatios, numberOfRatios); + } + +} \ No newline at end of file diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/KeyReadsFn.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/KeyReadsFn.java new file mode 100644 index 0000000..3444449 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/KeyReadsFn.java @@ -0,0 +1,115 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import com.google.api.services.genomics.model.Read; +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.Description; +import com.google.cloud.dataflow.sdk.options.PipelineOptions; +import com.google.cloud.dataflow.sdk.transforms.Aggregator; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.GroupByKey; +import com.google.cloud.dataflow.sdk.transforms.Sum.SumIntegerFn; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.genomics.utils.Contig; + +/* + * Takes a read and associates it with a Contig. + * This can be used to shard Reads so they can be written to disk in parallel. + * The size of the Contigs is determined by Options.getLociPerWritingShard. + */ +public class KeyReadsFn extends DoFn> { + + public static interface Options extends PipelineOptions { + @Description("Loci per writing shard") + @Default.Long(10000) + long getLociPerWritingShard(); + + void setLociPerWritingShard(long lociPerShard); + } + + private Aggregator readCountAggregator; + private Aggregator unmappedReadCountAggregator; + private long lociPerShard; + + public KeyReadsFn() { + readCountAggregator = createAggregator("Keyed reads", new SumIntegerFn()); + unmappedReadCountAggregator = createAggregator("Keyed unmapped reads", new SumIntegerFn()); + } + + @Override + public void startBundle(Context c) { + lociPerShard = c.getPipelineOptions() + .as(Options.class) + .getLociPerWritingShard(); + } + + @Override + public void processElement(DoFn>.ProcessContext c) + throws Exception { + final Read read = c.element(); + c.output( + KV.of( + shardKeyForRead(read, lociPerShard), + read)); + readCountAggregator.addValue(1); + if (isUnmapped(read)) { + unmappedReadCountAggregator.addValue(1); + } + } + + static boolean isUnmapped(Read read) { + if (read.getAlignment() == null || read.getAlignment().getPosition() == null) { + return true; + } + final String reference = read.getAlignment().getPosition().getReferenceName(); + if (reference == null || reference.isEmpty() || reference.equals("*")) { + return true; + } + return false; + } + + static Contig shardKeyForRead(Read read, long lociPerShard) { + String referenceName = null; + Long alignmentStart = null; + if (read.getAlignment() != null) { + if (read.getAlignment().getPosition() != null ) { + referenceName = read.getAlignment().getPosition().getReferenceName(); + alignmentStart = read.getAlignment().getPosition().getPosition(); + } + } + // If this read is unmapped but its mate is mapped, group them together. + if (referenceName == null || referenceName.isEmpty() || + referenceName.equals("*") || alignmentStart == null) { + if (read.getNextMatePosition() != null) { + referenceName = read.getNextMatePosition().getReferenceName(); + alignmentStart = read.getNextMatePosition().getPosition(); + } + } + if (referenceName == null || referenceName.isEmpty()) { + referenceName = "*"; + } + if (alignmentStart == null) { + alignmentStart = new Long(0); + } + return shardFromAlignmentStart(referenceName, alignmentStart, lociPerShard); + } + + static Contig shardFromAlignmentStart(String referenceName, long alignmentStart, long lociPerShard) { + final long shardStart = (alignmentStart / lociPerShard) * lociPerShard; + return new Contig(referenceName, shardStart, shardStart + lociPerShard); + } +} \ No newline at end of file diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/LikelihoodFn.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/LikelihoodFn.java new file mode 100644 index 0000000..f398a88 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/LikelihoodFn.java @@ -0,0 +1,175 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import com.google.cloud.genomics.dataflow.model.ReadCounts; +import com.google.cloud.genomics.dataflow.model.ReadQualityCount; +import com.google.cloud.genomics.dataflow.model.ReadQualityCount.Base; +import com.google.common.collect.ImmutableList; +import com.google.common.collect.ImmutableMap; +import com.google.genomics.v1.Position; + +import org.apache.commons.math3.analysis.UnivariateFunction; + +import java.util.ArrayList; +import java.util.Collections; +import java.util.Iterator; +import java.util.Map; + +/** + * Implementation of the likelihood function in equation (2) in + * G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, + * G. Abecasis, M. Boehnke,and H. M. Kang, Detecting and Estimating + * Contamination of Human DNA Samples in Sequencing and Array-Based Genotype + * Data, American journal of human genetics doi:10.1016/j.ajhg.2012.09.004 + * (volume 91 issue 5 pp.839 - 848) + * http://www.sciencedirect.com/science/article/pii/S0002929712004788 + */ +public class LikelihoodFn implements UnivariateFunction { + + /** Possible genotypes for a SNP with a single alternate */ + enum Genotype { + REF_HOMOZYGOUS, HETEROZYGOUS, NONREF_HOMOZYGOUS + } + /** Possible error statuses for a base in a read */ + enum ReadStatus { + CORRECT, ERROR + } + + static int toTableIndex(Base observed, Genotype trueGenotype, ReadStatus status) { + return observed.ordinal() + + Base.values().length * (status.ordinal() + + ReadStatus.values().length * trueGenotype.ordinal()); + } + + /* + * P_OBS_GIVEN_TRUTH contains the probability of observing a particular + * base (reference, non-reference, or other) given the true genotype + * and the error status of the read. See Table 1 of Jun et al. + */ + private static final ImmutableList P_OBS_GIVEN_TRUTH; + static { + final ImmutableList pTable = ImmutableList.of( + // Observed base + // REF NONREF OTHER + 1.0, 0.0, 0.0, // P(base | REF_HOMOZYGOUS, CORRECT) + 0.0, 1.0 / 3.0, 2.0 / 3.0, // P(base | REF_HOMOZYGOUS, ERROR) + 0.5, 0.5, 0.0, // P(base | HETEROZYGOUS, CORRECT) + 1.0 / 6.0, 1.0 / 6.0, 2.0 / 3.0, // P(base | HETEROZYGOUS, ERROR) + 0.0, 1.0, 0.0, // P(base | NONREF_HOMOZYGOUS, CORRECT) + 1.0 / 3.0, 0.0, 2.0 / 3.0); // P(base | NONREF_HOMOZYGOUS, ERROR) + Iterator itProb = pTable.iterator(); + ArrayList pCond = new ArrayList<>(); + pCond.addAll(Collections.nCopies( + Base.values().length * ReadStatus.values().length * Genotype.values().length, 0.0)); + for ( + Genotype g : ImmutableList.of(Genotype.REF_HOMOZYGOUS, Genotype.HETEROZYGOUS, + Genotype.NONREF_HOMOZYGOUS)) { + for (ReadStatus r : ImmutableList.of(ReadStatus.CORRECT, ReadStatus.ERROR)) { + for (Base b : ImmutableList.of(Base.REF, Base.NONREF, Base.OTHER)) { + pCond.set(toTableIndex(b, g, r), itProb.next()); + } + } + } + P_OBS_GIVEN_TRUTH = ImmutableList.copyOf(pCond); + } + + private final Map readCounts; + + /** + * Create a new LikelihoodFn instance for a given set of read counts. + * + * @param readCounts counts of reads by quality for each position of interest + */ + public LikelihoodFn(Map readCounts) { + // copy the map so the counts don't get changed out from under us + this.readCounts = ImmutableMap.copyOf(readCounts); + } + + /** + * Compute the probability of a genotype given the reference allele probability. + */ + private static double pGenotype(Genotype g, double refProb) { + switch(g) { + case REF_HOMOZYGOUS: + return refProb * refProb; + case HETEROZYGOUS: + return refProb * (1.0 - refProb); + case NONREF_HOMOZYGOUS: + return (1.0 - refProb) * (1.0 - refProb); + default: + throw new IllegalArgumentException("Illegal genotype"); + } + } + + /** + * Look up the probability of an observation conditioned on the underlying state. + */ + private static double probObsGivenTruth(Base observed, Genotype trueGenotype, + ReadStatus trueStatus) { + return P_OBS_GIVEN_TRUTH.get(toTableIndex(observed, trueGenotype, trueStatus)); + } + + /** + * Compute the likelihood of a contaminant fraction alpha. + * + *

See equation (2) in Jun et al. + */ + @Override + public double value(double alpha) { + double logLikelihood = 0.0; + for (ReadCounts rc : readCounts.values()) { + double refProb = rc.getRefFreq(); + + double pPosition = 0.0; + for (Genotype trueGenotype1 : Genotype.values()) { + double pGenotype1 = pGenotype(trueGenotype1, refProb); + for (Genotype trueGenotype2 : Genotype.values()) { + double pGenotype2 = pGenotype(trueGenotype2, refProb); + + double pObsGivenGenotype = 1.0; + + for (ReadQualityCount rqc : rc.getReadQualityCounts()) { + Base base = rqc.getBase(); + double pErr = phredToProb(rqc.getQuality()); + double pObs + = ((1.0 - alpha) + * probObsGivenTruth(base, trueGenotype1, ReadStatus.CORRECT) + + (alpha) + * probObsGivenTruth(base, trueGenotype2, ReadStatus.CORRECT) + ) * (1.0 - pErr) + + ((1.0 - alpha) + * probObsGivenTruth(base, trueGenotype1, ReadStatus.ERROR) + + (alpha) + * probObsGivenTruth(base, trueGenotype2, ReadStatus.ERROR) + ) * pErr; + pObsGivenGenotype *= Math.pow(pObs, rqc.getCount()); + } + pPosition += pObsGivenGenotype * pGenotype1 * pGenotype2; + } + } + logLikelihood += Math.log(pPosition); + } + return logLikelihood; + } + + /** + * Convert a Phred score to a probability. + */ + private static double phredToProb(int phred) { + return Math.pow(10.0, -(double) phred / 10.0); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/OutputPCoAFile.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/OutputPCoAFile.java new file mode 100644 index 0000000..532425d --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/OutputPCoAFile.java @@ -0,0 +1,99 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import com.google.cloud.dataflow.sdk.io.TextIO; +import com.google.cloud.dataflow.sdk.transforms.Combine; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.PTransform; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.transforms.Sum; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.dataflow.sdk.values.PDone; +import com.google.common.collect.BiMap; + +import java.util.ArrayList; +import java.util.List; + +/** + * Given a set of similar pair counts, this function aggregates the counts, + * runs Principal Coordinate Analysis, and writes the result to a tab-delimited GCS file which + * can be imported into Google Spreadsheets and rendered with a bubble graph. + * + * The input data must be for a similarity matrix which will be symmetric. This is not + * the same as Principal Component Analysis. +*/ +public class OutputPCoAFile extends PTransform, Long>>, PDone> { + + private static final Combine.CombineFn, Long>, + List, Long>>, Iterable, Long>>> TO_LIST = + toList(); + + private static Combine.CombineFn, Iterable> toList() { + return new Combine.CombineFn, Iterable>() { + + @Override public List addInput(List accumulator, X input) { + accumulator.add(input); + return accumulator; + } + + @Override public List createAccumulator() { + return new ArrayList<>(); + } + + @Override public Iterable extractOutput(List accumulator) { + return accumulator; + } + + @Override public List mergeAccumulators( + Iterable> accumulators) { + List merged = new ArrayList<>(); + for (List accumulator : accumulators) { + merged.addAll(accumulator); + } + return merged; + } + }; + } + + private BiMap dataIndices; + private final String outputFile; + + public OutputPCoAFile(BiMap dataIndices, String outputFile) { + this.dataIndices = dataIndices; + this.outputFile = outputFile; + } + + @Override + public PDone apply(PCollection, Long>> similarPairs) { + return similarPairs + .apply(Sum.>longsPerKey()) + .apply(Combine.globally(TO_LIST)) + .apply(ParDo.named("PCoAAnalysis").of(new PCoAnalysis(dataIndices))) + .apply(ParDo.named("FormatGraphData") + .of(new DoFn, String>() { + @Override + public void processElement(ProcessContext c) throws Exception { + Iterable graphResults = c.element(); + for (PCoAnalysis.GraphResult result : graphResults) { + c.output(result.toString()); + } + } + })) + .apply(TextIO.Write.named("WriteCounts").to(outputFile)); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/PCoAnalysis.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/PCoAnalysis.java new file mode 100644 index 0000000..16cff4c --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/PCoAnalysis.java @@ -0,0 +1,213 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ + +package com.google.cloud.genomics.dataflow.functions; + +import java.io.Serializable; +import java.util.Collection; +import java.util.List; + +import Jama.EigenvalueDecomposition; +import Jama.Matrix; + +import com.google.api.client.util.Lists; +import com.google.api.client.util.Preconditions; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.common.collect.BiMap; +import com.google.common.collect.ImmutableList; + +/** + * This function runs a Principal Coordinate Analysis inside of a SeqDo. + * It can not be parallelized. + * + * See http://en.wikipedia.org/wiki/PCoA for more information. + * + * Note that this is not the same as + * Principal Component Analysis (http://en.wikipedia.org/wiki/Principal_component_analysis) + * + * The input data to this algorithm must be for a similarity matrix - and the + * resulting matrix must be symmetric. + * + * Input: KV(KV(dataName, dataName), count of how similar the data pair is) + * Output: GraphResults - an x/y pair and a label + * + * Example input for a tiny dataset of size 2: + * + * KV(KV(data1, data1), 5) + * KV(KV(data1, data2), 2) + * KV(KV(data2, data2), 5) + * KV(KV(data2, data1), 2) + */ +public class PCoAnalysis extends DoFn, Long>>, + Iterable> { + + public static class GraphResult implements Serializable { + + public double graphX; + public double graphY; + public String name; + + public GraphResult(String name, double x, double y) { + this.name = name; + this.graphX = Math.floor(x * 100) / 100; + this.graphY = Math.floor(y * 100) / 100; + } + + @Override public String toString() { + return String.format("%s\t\t%s\t%s", name, graphX, graphY); + } + + public static GraphResult fromString(String tsv) { + Preconditions.checkNotNull(tsv); + String[] tokens = tsv.split("[\\s\t]+"); + Preconditions.checkState(3 == tokens.length, + "Expected three values in serialized GraphResult but found %d", tokens.length); + return new GraphResult(tokens[0], + Double.parseDouble(tokens[1]), + Double.parseDouble(tokens[2])); + } + + @Override // auto-generated via eclipse + public int hashCode() { + final int prime = 31; + int result = 1; + long temp; + temp = Double.doubleToLongBits(graphX); + result = prime * result + (int) (temp ^ (temp >>> 32)); + temp = Double.doubleToLongBits(graphY); + result = prime * result + (int) (temp ^ (temp >>> 32)); + result = prime * result + ((name == null) ? 0 : name.hashCode()); + return result; + } + + @Override // auto-generated via eclipse + public boolean equals(Object obj) { + if (this == obj) + return true; + if (obj == null) + return false; + if (getClass() != obj.getClass()) + return false; + GraphResult other = (GraphResult) obj; + if (name == null) { + if (other.name != null) + return false; + } else if (!name.equals(other.name)) + return false; + if (Double.doubleToLongBits(graphX) != Double.doubleToLongBits(other.graphX)) + return false; + if (Double.doubleToLongBits(graphY) != Double.doubleToLongBits(other.graphY)) + return false; + return true; + } + } + + private BiMap dataIndices; + + public PCoAnalysis(BiMap dataIndices) { + this.dataIndices = dataIndices; + } + + // Convert the similarity matrix to an Eigen matrix. + private List getPcaData(double[][] data, BiMap dataNames) { + int rows = data.length; + int cols = data.length; + + // Center the similarity matrix. + double matrixSum = 0; + double[] rowSums = new double[rows]; + for (int i = 0; i < rows; i++) { + for (int j = 0; j < cols; j++) { + matrixSum += data[i][j]; + rowSums[i] += data[i][j]; + } + } + double matrixMean = matrixSum / rows / cols; + for (int i = 0; i < rows; i++) { + for (int j = 0; j < cols; j++) { + double rowMean = rowSums[i] / rows; + double colMean = rowSums[j] / rows; + data[i][j] = data[i][j] - rowMean - colMean + matrixMean; + } + } + + + // Determine the eigenvectors, and scale them so that their + // sum of squares equals their associated eigenvalue. + Matrix matrix = new Matrix(data); + EigenvalueDecomposition eig = matrix.eig(); + Matrix eigenvectors = eig.getV(); + double[] realEigenvalues = eig.getRealEigenvalues(); + + for (int j = 0; j < eigenvectors.getColumnDimension(); j++) { + double sumSquares = 0; + for (int i = 0; i < eigenvectors.getRowDimension(); i++) { + sumSquares += eigenvectors.get(i, j) * eigenvectors.get(i, j); + } + for (int i = 0; i < eigenvectors.getRowDimension(); i++) { + eigenvectors.set(i, j, eigenvectors.get(i,j) * Math.sqrt(realEigenvalues[j] / sumSquares)); + } + } + + + // Find the indices of the top two eigenvalues. + int maxIndex = -1; + int secondIndex = -1; + double maxEigenvalue = 0; + double secondEigenvalue = 0; + + for (int i = 0; i < realEigenvalues.length; i++) { + double eigenvector = realEigenvalues[i]; + if (eigenvector > maxEigenvalue) { + secondEigenvalue = maxEigenvalue; + secondIndex = maxIndex; + maxEigenvalue = eigenvector; + maxIndex = i; + } else if (eigenvector > secondEigenvalue) { + secondEigenvalue = eigenvector; + secondIndex = i; + } + } + + + // Return projected data + List results = Lists.newArrayList(); + for (int i = 0; i < rows; i++) { + results.add(new GraphResult(dataNames.get(i), + eigenvectors.get(i, maxIndex), eigenvectors.get(i, secondIndex))); + } + + return results; + } + + @Override public void processElement(ProcessContext context) { + Collection, Long>> element = ImmutableList.copyOf(context.element()); + + int dataSize = dataIndices.size(); + double[][] matrixData = new double[dataSize][dataSize]; + for (KV, Long> entry : element) { + int d1 = dataIndices.get(entry.getKey().getKey()); + int d2 = dataIndices.get(entry.getKey().getValue()); + double value = entry.getValue(); + matrixData[d1][d2] = value; + if (d1 != d2) { + matrixData[d2][d1] = value; + } + } + context.output(getPcaData(matrixData, dataIndices.inverse())); + } +} \ No newline at end of file diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/SharedAllelesRatioCalculator.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/SharedAllelesRatioCalculator.java new file mode 100644 index 0000000..f5d7a1a --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/SharedAllelesRatioCalculator.java @@ -0,0 +1,43 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import com.google.genomics.v1.VariantCall; + +/** + * See this + * pdf and video descriptions of + * Identity By State (IBS) for the basis of this implementation. + */ +public class SharedAllelesRatioCalculator implements CallSimilarityCalculator { + + // TODO: Double check that the following is the right way of computing the IBS + // scores when the number of alleles is different than 2 and when the genotypes are unphased. + @Override + public double similarity(VariantCall call1, VariantCall call2) { + int minNumberOfGenotypes = Math.min(call1.getGenotypeCount(), call2.getGenotypeCount()); + int numberOfSharedAlleles = 0; + for (int i = 0; i < minNumberOfGenotypes; ++i) { + if (call1.getGenotype(i) == call2.getGenotype(i)) { + ++numberOfSharedAlleles; + } + } + int maxNumberOfGenotypes = Math.max(call1.getGenotypeCount(), call2.getGenotypeCount()); + return (double) numberOfSharedAlleles / maxNumberOfGenotypes; + } + + +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/SharedAllelesRatioCalculatorFactory.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/SharedAllelesRatioCalculatorFactory.java new file mode 100644 index 0000000..8c2b211 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/SharedAllelesRatioCalculatorFactory.java @@ -0,0 +1,25 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +public class SharedAllelesRatioCalculatorFactory implements CallSimilarityCalculatorFactory { + + @Override + public SharedAllelesRatioCalculator get(boolean isReferenceMajor) { + return new SharedAllelesRatioCalculator(); + } + +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/SharedMinorAllelesCalculator.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/SharedMinorAllelesCalculator.java new file mode 100644 index 0000000..c6e86cc --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/SharedMinorAllelesCalculator.java @@ -0,0 +1,60 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import com.google.common.base.Predicate; +import com.google.common.collect.Iterables; +import com.google.genomics.v1.VariantCall; + +/** + * Computes the similarity of two calls based on whether they share a minor allele or not. + */ +public class SharedMinorAllelesCalculator implements CallSimilarityCalculator { + + private final boolean isReferenceMajor; + + public SharedMinorAllelesCalculator(boolean isReferenceMajor) { + this.isReferenceMajor = isReferenceMajor; + } + + private boolean hasMinorAllele(VariantCall call) { + return Iterables.any(call.getGenotypeList(), new Predicate() { + + @Override + public boolean apply(Integer genotype) { + if (isReferenceMajor) { + return genotype > 0; + } else { + return genotype == 0; + } + } + + }); + } + + @Override + public double similarity(VariantCall call1, VariantCall call2) { + if (call1.getCallSetName().equals(call2.getCallSetName())) { + return 1.0; + } + if (hasMinorAllele(call1) && hasMinorAllele(call2)) { + return 1.0; + } else { + return 0.0; + } + } + +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/SharedMinorAllelesCalculatorFactory.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/SharedMinorAllelesCalculatorFactory.java new file mode 100644 index 0000000..a760300 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/SharedMinorAllelesCalculatorFactory.java @@ -0,0 +1,25 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +public class SharedMinorAllelesCalculatorFactory implements CallSimilarityCalculatorFactory { + + @Override + public SharedMinorAllelesCalculator get(boolean isReferenceMajor) { + return new SharedMinorAllelesCalculator(isReferenceMajor); + } + +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/WriteShardFn.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/WriteShardFn.java new file mode 100644 index 0000000..123bf36 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/WriteShardFn.java @@ -0,0 +1,149 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import htsjdk.samtools.BAMBlockWriter; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.BlockCompressedStreamConstants; + +import java.io.IOException; +import java.io.OutputStream; +import java.nio.channels.Channels; +import java.util.logging.Logger; + +import com.google.api.services.genomics.model.Read; +import com.google.api.services.storage.Storage; +import com.google.cloud.dataflow.sdk.transforms.Aggregator; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.Sum.SumIntegerFn; +import com.google.cloud.dataflow.sdk.util.GcsUtil; +import com.google.cloud.dataflow.sdk.util.Transport; +import com.google.cloud.dataflow.sdk.util.gcsfs.GcsPath; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.dataflow.sdk.values.PCollectionView; +import com.google.cloud.genomics.dataflow.pipelines.ShardedBAMWriting.HeaderInfo; +import com.google.cloud.genomics.dataflow.utils.GCSOptions; +import com.google.cloud.genomics.dataflow.utils.GCSOutputOptions; +import com.google.cloud.genomics.dataflow.utils.TruncatedOutputStream; +import com.google.cloud.genomics.utils.Contig; +import com.google.cloud.genomics.utils.ReadUtils; + +/* + * Takes a set of Reads associated with a Contig and writes them to a BAM file. + */ +public class WriteShardFn extends DoFn>, String> { + + public static interface Options extends GCSOutputOptions {} + + private static final int MAX_RETRIES_FOR_WRITING_A_SHARD = 4; + private static final String BAM_INDEX_FILE_MIME_TYPE = "application/octet-stream"; + private static final Logger LOG = Logger.getLogger(WriteShardFn.class.getName()); + + final PCollectionView headerView; + Storage.Objects storage; + Aggregator readCountAggregator; + Aggregator unmappedReadCountAggregator; + + public WriteShardFn(final PCollectionView headerView) { + this.headerView = headerView; + readCountAggregator = createAggregator("Written reads", new SumIntegerFn()); + unmappedReadCountAggregator = createAggregator("Written unmapped reads", new SumIntegerFn()); + } + + @Override + public void startBundle(DoFn>, String>.Context c) throws IOException { + storage = Transport.newStorageClient(c.getPipelineOptions().as(GCSOptions.class)).build().objects(); + } + + @Override + public void processElement(DoFn>, String>.ProcessContext c) + throws Exception { + final HeaderInfo headerInfo = c.sideInput(headerView); + final KV> shard = c.element(); + final Contig shardContig = shard.getKey(); + final Iterable reads = shard.getValue(); + final boolean isFirstShard = shardContig.equals(headerInfo.firstShard); + + int numRetriesLeft = MAX_RETRIES_FOR_WRITING_A_SHARD; + boolean done = false; + do { + try { + final String writeResult = writeShard(headerInfo.header, + shardContig, reads, + c.getPipelineOptions().as(Options.class), + isFirstShard); + c.output(writeResult); + done = true; + } catch (IOException iox) { + LOG.warning("Write shard failed for " + shardContig + ": " + iox.getMessage()); + if (--numRetriesLeft <= 0) { + LOG.warning("No more retries - failing the task for " + shardContig); + throw iox; + } + } + } while (!done); + LOG.info("Finished writing " + shardContig); + } + + String writeShard(SAMFileHeader header, Contig shardContig, Iterable reads, + Options options, boolean isFirstShard) throws IOException { + final String outputFileName = options.getOutput(); + final String shardName = outputFileName + "-" + shardContig.referenceName + + ":" + String.format("%012d", shardContig.start) + "-" + + String.format("%012d", shardContig.end); + LOG.info("Writing shard file " + shardName); + final OutputStream outputStream = + Channels.newOutputStream( + new GcsUtil.GcsUtilFactory().create(options) + .create(GcsPath.fromUri(shardName), + BAM_INDEX_FILE_MIME_TYPE)); + int count = 0; + int countUnmapped = 0; + // Use a TruncatedOutputStream to avoid writing the empty gzip block that + // indicates EOF. + final BAMBlockWriter bw = new BAMBlockWriter(new TruncatedOutputStream( + outputStream, BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK.length), + null /*file*/); + // If reads are unsorted then we do not care about their order + // otherwise we need to sort them as we write. + final boolean treatReadsAsPresorted = + header.getSortOrder() == SAMFileHeader.SortOrder.unsorted; + bw.setSortOrder(header.getSortOrder(), treatReadsAsPresorted); + bw.setHeader(header); + if (isFirstShard) { + LOG.info("First shard - writing header to " + shardName); + bw.writeHeader(header); + } + for (Read read : reads) { + SAMRecord samRecord = ReadUtils.makeSAMRecord(read, header); + if (samRecord.getReadUnmappedFlag()) { + if (!samRecord.getMateUnmappedFlag()) { + samRecord.setReferenceName(samRecord.getMateReferenceName()); + samRecord.setAlignmentStart(samRecord.getMateAlignmentStart()); + } + countUnmapped++; + } + bw.addAlignment(samRecord); + count++; + } + bw.close(); + LOG.info("Wrote " + count + " reads, " + countUnmapped + " umapped, into " + shardName); + readCountAggregator.addValue(count); + unmappedReadCountAggregator.addValue(countUnmapped); + return shardName; + } +} \ No newline at end of file diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/grpc/JoinNonVariantSegmentsWithVariants.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/grpc/JoinNonVariantSegmentsWithVariants.java new file mode 100644 index 0000000..9618e75 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/grpc/JoinNonVariantSegmentsWithVariants.java @@ -0,0 +1,194 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions.grpc; + +import java.util.Collections; +import java.util.Comparator; +import java.util.Iterator; +import java.util.LinkedList; +import java.util.List; + +import com.google.api.client.util.Lists; +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.Description; +import com.google.cloud.dataflow.sdk.options.PipelineOptions; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.GroupByKey; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.genomics.utils.grpc.VariantUtils; +import com.google.common.annotations.VisibleForTesting; +import com.google.common.base.Function; +import com.google.common.base.Preconditions; +import com.google.common.collect.Ordering; +import com.google.genomics.v1.Variant; +import com.google.genomics.v1.Variant.Builder; + +/** + * The transforms in this class convert data with non-variant segments (such as data that was in + * source format Genome VCF (gVCF) or Complete Genomics) to variant-only data with calls from + * non-variant-segments merged into the variants with which they overlap. + * + * This is currently done only for SNP variants. Indels and structural variants are left as-is. + * + * SCALING: For a large cohort with many, many more rare variants we may wish to instead modify the + * logic here to summarize the number of calls that match the reference for each variant instead of + * adding those individual calls to the record. + * + */ +public class JoinNonVariantSegmentsWithVariants { + + public static interface Options extends PipelineOptions { + @Description("If querying a dataset with non-variant segments (such as Complete Genomics data " + + "or data in Genome VCF (gVCF) format), specify this flag so that the pipeline correctly " + + "takes into account non-variant segment records that overlap variants within the dataset.") + @Default.Boolean(false) + boolean getHasNonVariantSegments(); + void setHasNonVariantSegments(boolean hasNonVariantSegments); + + @Description("Genomic window \"bin\" size to use for data containing non-variant segments when " + + "joining those non-variant segment records with variant records.") + @Default.Integer(1000) + int getBinSize(); + void setBinSize(int binSize); + + public static class Methods { + public static void validateOptions(Options options) { + Preconditions.checkArgument(0 < options.getBinSize(), "binSize must be greater than zero"); + } + } + } + + /** + * Use this transform for correct handling of data with non-variant segments in DataFlow jobs that + * consider not only calls that have the variant but also those that match the reference at that + * variant position. + * + * @param input PCollection of variants to process. + * @return PCollection of variant-only Variant objects with calls from non-variant-segments + * merged into the variants with which they overlap. + */ + public static PCollection joinVariantsTransform(PCollection input) { + return joinVariants(input); + } + + private static PCollection joinVariants(PCollection input) { + return input + .apply(ParDo.of(new JoinNonVariantSegmentsWithVariants.BinVariants())) + .apply(GroupByKey., Variant>create()) + .apply(ParDo.of(new JoinNonVariantSegmentsWithVariants.MergeVariants())); + } + + private static final Ordering BY_START = Ordering.natural().onResultOf( + new Function() { + @Override + public Long apply(Variant variant) { + return variant.getStart(); + } + }); + + private static final Ordering BY_FIRST_OF_ALTERNATE_BASES = Ordering.natural() + .nullsFirst().onResultOf(new Function() { + @Override + public String apply(Variant variant) { + if (null == variant.getAlternateBasesList() || variant.getAlternateBasesList().isEmpty()) { + return null; + } + return variant.getAlternateBases(0); + } + }); + + // Special-purpose comparator for use in dealing with both variant and non-variant segment data. + // Sort by start position ascending and ensure that if a variant and a ref-matching block are at + // the same position, the non-variant segment record comes first. + @VisibleForTesting + static final Comparator NON_VARIANT_SEGMENT_COMPARATOR = BY_START + .compound(BY_FIRST_OF_ALTERNATE_BASES); + + public static final class BinVariants extends DoFn, Variant>> { + + public static final long getStartBin(int binSize, Variant variant) { + // Round down to the nearest integer + return Math.round(Math.floor(variant.getStart() / binSize)); + } + + public static final long getEndBin(int binSize, Variant variant) { + // Round down to the nearest integer + return Math.round(Math.floor(variant.getEnd() / binSize)); + } + + @Override + public void processElement(ProcessContext context) { + Options options = + context.getPipelineOptions().as(Options.class); + Variant variant = context.element(); + long startBin = getStartBin(options.getBinSize(), variant); + long endBin = + VariantUtils.IS_NON_VARIANT_SEGMENT.apply(variant) ? getEndBin(options.getBinSize(), + variant) : startBin; + for (long bin = startBin; bin <= endBin; bin++) { + context.output(KV.of(KV.of(variant.getReferenceName(), bin), variant)); + } + } + } + + public static final class MergeVariants extends + DoFn, Iterable>, Variant> { + + @Override + public void processElement(ProcessContext context) { + + // The upper bound on number of variants in the iterable is dependent upon the binSize + // used in the prior step to construct the key. + KV, Iterable> kv = context.element(); + + List records = Lists.newArrayList(kv.getValue()); + // The sort order is critical here so that candidate overlapping reference matching blocks + // occur prior to any variants they may overlap. + Collections.sort(records, NON_VARIANT_SEGMENT_COMPARATOR); + + // The upper bound on potential overlaps is the sample size plus the number of + // block records that occur between actual variants. + List blockRecords = new LinkedList<>(); + + for (Variant record : records) { + if (!VariantUtils.IS_NON_VARIANT_SEGMENT.apply(record)) { + Builder updatedRecord = Variant.newBuilder(record); + // TODO: determine and implement the correct criteria for overlaps of non-SNP variants + if (VariantUtils.IS_SNP.apply(record)) { + for (Iterator iterator = blockRecords.iterator(); iterator.hasNext();) { + Variant blockRecord = iterator.next(); + if (JoinNonVariantSegmentsWithVariants.isOverlapping(blockRecord, record)) { + updatedRecord.addAllCalls(blockRecord.getCallsList()); + } else { + // Remove the current element from the iterator and the list since it is + // left of the genomic region we are currently working on due to our sort.. + iterator.remove(); + } + } + } + context.output(updatedRecord.build()); + } else { + blockRecords.add(record); + } + } + } + } + + public static boolean isOverlapping(Variant blockRecord, Variant variant) { + return blockRecord.getStart() <= variant.getStart() + && blockRecord.getEnd() >= variant.getStart() + 1; + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/model/Allele.java b/src/main/java/com/google/cloud/genomics/dataflow/model/Allele.java new file mode 100644 index 0000000..260afcf --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/model/Allele.java @@ -0,0 +1,40 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.model; + +/** + * A small container to store the alleles at a location + * + */ +public class Allele { + String referenceName; + long position; + String allele; + + public Allele(String referenceName, long position, String allele) { + this.referenceName = referenceName; + this.position = position; + this.allele = allele; + } + + public String getReferenceName() { + return referenceName; + } + + public String getAllele() { + return allele; + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/model/AlleleFreq.java b/src/main/java/com/google/cloud/genomics/dataflow/model/AlleleFreq.java new file mode 100644 index 0000000..da99231 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/model/AlleleFreq.java @@ -0,0 +1,61 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.model; + +import com.google.api.client.json.GenericJson; +import com.google.cloud.dataflow.sdk.coders.DefaultCoder; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; + +import java.util.List; + +/** + * Contains frequency for a set of alleles for a single position on a single chromosome. + * Used in VerifyBamId. + */ +@DefaultCoder(GenericJsonCoder.class) +public class AlleleFreq extends GenericJson { + // Strings of length 1 of one of the following bases: ['A', 'C', 'T', 'G']. + private String refBases; + // List of length 1 of a String of length 1 of one of the following bases: ['A', 'C', 'T', 'G']. + private List altBases; + // Frequency for a set of alleles for the given position on the given chromosome + // in the range [0,1]. + private double refFreq; + + public String getRefBases() { + return refBases; + } + + public void setRefBases(String refBases) { + this.refBases = refBases; + } + + public List getAltBases() { + return altBases; + } + + public void setAltBases(List altBases) { + this.altBases = altBases; + } + + public double getRefFreq() { + return refFreq; + } + + public void setRefFreq(double refFreq) { + this.refFreq = refFreq; + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/model/PosRgsMq.java b/src/main/java/com/google/cloud/genomics/dataflow/model/PosRgsMq.java new file mode 100644 index 0000000..0bc21c1 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/model/PosRgsMq.java @@ -0,0 +1,117 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.model; + +import com.google.api.client.json.GenericJson; +import com.google.api.client.util.Key; +import com.google.api.client.util.Value; +import com.google.api.services.genomics.model.Position; +import com.google.cloud.dataflow.sdk.coders.AvroCoder; +import com.google.cloud.dataflow.sdk.coders.DefaultCoder; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import java.util.Objects; + +/** + * Wrapper class for Position, ReadGroupSetId and mapping quality objects for use in the + * CalculateCoverage pipeline + */ +@DefaultCoder(GenericJsonCoder.class) +public class PosRgsMq extends GenericJson { + + @Key + private Position pos; + @Key + private String rgsId; + @Key + private MappingQuality mq; + + /** + * MappingQuality enum that contains the 4 possible MappingQuality types (Low(L), Medium(M), + * High(H), and All(A)). + */ + @DefaultCoder(AvroCoder.class) + public enum MappingQuality {@Value L, @Value M, @Value H, @Value A} + + public PosRgsMq() { + this.pos = new Position().setPosition(0L).setReferenceName(""); + this.rgsId = ""; + this.mq = MappingQuality.A; + } + + public PosRgsMq(Position pos, String rgsId, MappingQuality mq) { + this.pos = pos; + this.rgsId = rgsId; + this.mq = mq; + } + + public Position getPos() { + return pos; + } + + public void setPos(Position pos) { + this.pos = pos; + } + + public String getRgsId() { + return rgsId; + } + + public void setRgsId(String rgsId) { + this.rgsId = rgsId; + } + + public MappingQuality getMq() { + return mq; + } + + public void setMq(MappingQuality mq) { + this.mq = mq; + } + + @Override + public boolean equals(Object o) { + if (o == null) { + return false; + } + if (o == this) { + return true; + } + if (!(o instanceof PosRgsMq)) { + return false; + } + PosRgsMq test = (PosRgsMq) o; + return test.pos.equals(this.pos) && test.rgsId.equals(this.rgsId) && test.mq.equals(this.mq); + } + + @Override + public int hashCode() { + int hash = 7; + hash = 19 * hash + Objects.hashCode(this.pos); + hash = 19 * hash + Objects.hashCode(this.rgsId); + hash = 19 * hash + Objects.hashCode(this.mq); + return hash; + } + + @Override + public PosRgsMq set(String fieldName, Object value) { + return (PosRgsMq) super.set(fieldName, value); + } + + @Override + public PosRgsMq clone() { + return (PosRgsMq) super.clone(); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/model/ReadBaseQuality.java b/src/main/java/com/google/cloud/genomics/dataflow/model/ReadBaseQuality.java new file mode 100644 index 0000000..ca30cef --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/model/ReadBaseQuality.java @@ -0,0 +1,79 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.model; + +import com.google.api.client.json.GenericJson; +import com.google.cloud.dataflow.sdk.coders.DefaultCoder; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import java.util.Objects; + +/** + * Data on a single base in a read, used for pileup. + */ +@DefaultCoder(GenericJsonCoder.class) +public class ReadBaseQuality extends GenericJson { + + private String base; + private int quality; + + public ReadBaseQuality() { + this.base = ""; + } + + public ReadBaseQuality(String base, int quality) { + this.base = base; + this.quality = quality; + } + + public String getBase() { + return base; + } + + public void setBase(String base) { + this.base = base; + } + + public int getQuality() { + return quality; + } + + public void setQuality(int quality) { + this.quality = quality; + } + + @Override + public boolean equals(Object o) { + if (o == null) { + return false; + } + if (o == this) { + return true; + } + if (!(o instanceof ReadBaseQuality)) { + return false; + } + ReadBaseQuality test = (ReadBaseQuality) o; + return test.base.equals(this.base) && test.quality == this.quality; + } + + @Override + public int hashCode() { + int hash = 3; + hash = 37 * hash + Objects.hashCode(this.base); + hash = 37 * hash + this.quality; + return hash; + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/model/ReadBaseWithReference.java b/src/main/java/com/google/cloud/genomics/dataflow/model/ReadBaseWithReference.java new file mode 100644 index 0000000..6ca1764 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/model/ReadBaseWithReference.java @@ -0,0 +1,92 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.model; + +import java.util.Objects; + +import com.google.genomics.v1.Position; + +/** + * Data on a single base in a read connected with it reference data. + */ +public class ReadBaseWithReference { + + private ReadBaseQuality rbq; + private String refBase; + private Position refPosition; + + public ReadBaseWithReference() { + this.rbq = new ReadBaseQuality(); + this.refBase = ""; + this.refPosition = Position.newBuilder().setPosition(0L).setReferenceName("").build(); + } + + public ReadBaseWithReference(ReadBaseQuality rbq, String refBase, Position refPosition) { + this.rbq = rbq; + this.refBase = refBase; + this.refPosition = refPosition; + } + + public String getRefBase() { + return refBase; + } + + public void setRefBase(String refBase) { + this.refBase = refBase; + } + + public Position getRefPosition() { + return refPosition; + } + + public void setRefPosition(Position refPosition) { + this.refPosition = refPosition; + } + + public ReadBaseQuality getRbq() { + return rbq; + } + + public void setRbq(ReadBaseQuality rbq) { + this.rbq = rbq; + } + + @Override + public int hashCode() { + int hash = 7; + hash = 89 * hash + Objects.hashCode(this.rbq); + hash = 89 * hash + Objects.hashCode(this.refBase); + hash = 89 * hash + Objects.hashCode(this.refPosition); + return hash; + } + + @Override + public boolean equals(Object other) { + if (other == null) { + return false; + } + if (other == this) { + return true; + } + if (!(other instanceof ReadBaseWithReference)) { + return false; + } + ReadBaseWithReference test = (ReadBaseWithReference) other; + return test.rbq.equals(this.rbq) && test.refBase.equals(this.refBase) + && test.refPosition.equals(this.refPosition); + } + +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/model/ReadCounts.java b/src/main/java/com/google/cloud/genomics/dataflow/model/ReadCounts.java new file mode 100644 index 0000000..b591984 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/model/ReadCounts.java @@ -0,0 +1,69 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.model; + +import com.google.api.client.json.GenericJson; +import com.google.api.client.util.Lists; +import com.google.cloud.dataflow.sdk.coders.DefaultCoder; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import com.google.cloud.genomics.dataflow.model.ReadQualityCount.Base; + +import java.util.List; + +/** + * Counts of reads for a single SNP with a single alternate value for use in the + * VerifyBamId pipeline. For each SNP, we accumulate counts of bases and quality scores + * for associated aligned reads. + */ +@DefaultCoder(GenericJsonCoder.class) +public class ReadCounts extends GenericJson { + /** + * The count for a single base and quality score is stored in a ReadQualityCount object. + */ + private List readQualityCounts = Lists.newArrayList(); + /** + * refFreq contains the population frequency of the reference allele. + */ + private double refFreq; + + public List getReadQualityCounts() { + return readQualityCounts; + } + + public void setReadQualityCounts(List readQualityCounts) { + this.readQualityCounts = readQualityCounts; + } + + public void addReadQualityCount(Base base, int quality, long count) { + ReadQualityCount rqc = new ReadQualityCount(); + rqc.setBase(base); + rqc.setCount(count); + rqc.setQuality(quality); + this.readQualityCounts.add(rqc); + } + + public void addReadQualityCount(ReadQualityCount rqc) { + this.readQualityCounts.add(rqc); + } + + public double getRefFreq() { + return refFreq; + } + + public void setRefFreq(double refFreq) { + this.refFreq = refFreq; + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/model/ReadQualityCount.java b/src/main/java/com/google/cloud/genomics/dataflow/model/ReadQualityCount.java new file mode 100644 index 0000000..7cf0669 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/model/ReadQualityCount.java @@ -0,0 +1,63 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.model; + +/** + * This class is used to count the number of reads aligned to a SNP that show the reference base, + * the non-reference base, some other base, or an unknown base. Within each category, we count the + * number with each quality score. + * + * For example, we might have 2 reads that show the reference base with quality 10, 5 reads that + * show the non-reference base with quality 60, and 1 read that shows a different nucleotide with + * quality 0. + */ +public class ReadQualityCount { + + private Base base; + private int quality; + private long count; + + /** + * Which type of Base this ReadQualityCount represents. + */ + public enum Base { + UNKNOWN, REF, NONREF, OTHER + }; + + public Base getBase() { + return base; + } + + public void setBase(Base base) { + this.base = base; + } + + public int getQuality() { + return quality; + } + + public void setQuality(int quality) { + this.quality = quality; + } + + public long getCount() { + return count; + } + + public void setCount(long count) { + this.count = count; + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/AnnotateVariants.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/AnnotateVariants.java new file mode 100644 index 0000000..1d2b86d --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/AnnotateVariants.java @@ -0,0 +1,362 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import htsjdk.samtools.util.IntervalTree; +import htsjdk.samtools.util.IntervalTree.Node; + +import java.io.IOException; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.concurrent.TimeUnit; +import java.util.logging.Logger; + +import com.google.api.client.util.Strings; +import com.google.api.services.genomics.Genomics; +import com.google.api.services.genomics.model.Annotation; +import com.google.api.services.genomics.model.AnnotationSet; +import com.google.api.services.genomics.model.ListBasesResponse; +import com.google.api.services.genomics.model.QueryRange; +import com.google.api.services.genomics.model.RangePosition; +import com.google.api.services.genomics.model.SearchAnnotationsRequest; +import com.google.api.services.genomics.model.SearchVariantsRequest; +import com.google.api.services.genomics.model.Variant; +import com.google.api.services.genomics.model.VariantAnnotation; +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.io.TextIO; +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.Description; +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.dataflow.sdk.transforms.Create; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.GroupByKey; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import com.google.cloud.genomics.dataflow.utils.AnnotationUtils; +import com.google.cloud.genomics.dataflow.utils.AnnotationUtils.VariantEffect; +import com.google.cloud.genomics.dataflow.utils.GCSOutputOptions; +import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; +import com.google.cloud.genomics.dataflow.utils.ShardOptions; +import com.google.cloud.genomics.utils.GenomicsFactory; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.cloud.genomics.utils.Paginator; +import com.google.cloud.genomics.utils.ShardBoundary; +import com.google.cloud.genomics.utils.ShardUtils; +import com.google.cloud.genomics.utils.VariantUtils; +import com.google.common.base.Joiner; +import com.google.common.base.Stopwatch; +import com.google.common.collect.ArrayListMultimap; +import com.google.common.collect.FluentIterable; +import com.google.common.collect.ImmutableList; +import com.google.common.collect.ListMultimap; +import com.google.common.collect.Maps; +import com.google.common.collect.Range; + +/** + * Demonstrates a simple variant annotation program which takes + * {@code VariantSet}s and {@code AnnotationSet}s as input and emits + * {@code VariantAnnotation}s. This program is intended to serve as an example + * of how a variant annotation program can be structured to run in parallel, + * operating over Google Genomics input sources; the current output has limited + * biological significance. + * + * Currently only annotates SNPs and uses the following two methods: + *

    + *
  • Determines the effect of the provided variants on the provided + * transcripts, if any. A result is only emitted for a subset of cases where + * the variant appears to cause a coding change in the transcript. + *
  • Performs an exact match join on the provided existing variant + * annotations, if any. + *
+ * + * See http://googlegenomics.readthedocs.org/en/latest/use_cases/annotate_variants/google_genomics_annotation.html + * for running instructions. + */ +public final class AnnotateVariants extends DoFn> { + + public static interface Options extends ShardOptions, GCSOutputOptions { + + @Description("The ID of the Google Genomics variant set this pipeline is accessing. " + + "Defaults to 1000 Genomes.") + @Default.String("10473108253681171589") + String getVariantSetId(); + + void setVariantSetId(String variantSetId); + + @Description("The IDs of the Google Genomics call sets this pipeline is working with, comma " + + "delimited.Defaults to 1000 Genomes HG00261.") + @Default.String("10473108253681171589-0") + String getCallSetIds(); + void setCallSetIds(String callSetIds); + + @Description("The IDs of the Google Genomics transcript sets this pipeline is working with, " + + "comma delimited. Defaults to UCSC refGene (hg19).") + @Default.String("CIjfoPXj9LqPlAEQ5vnql4KewYuSAQ") + String getTranscriptSetIds(); + void setTranscriptSetIds(String transcriptSetIds); + + @Description("The IDs of the Google Genomics variant annotation sets this pipeline is working " + + "with, comma delimited. Defaults to ClinVar (GRCh37).") + @Default.String("CILSqfjtlY6tHxC0nNH-4cu-xlQ") + String getVariantAnnotationSetIds(); + void setVariantAnnotationSetIds(String variantAnnotationSetIds); + + public static class Methods { + public static void validateOptions(Options options) { + GCSOutputOptions.Methods.validateOptions(options); + } + } + + } + + private static final Logger LOG = Logger.getLogger(AnnotateVariants.class.getName()); + private static final int VARIANTS_PAGE_SIZE = 5000; + private static final String VARIANT_FIELDS + = "nextPageToken,variants(id,referenceName,start,end,alternateBases,referenceBases)"; + + private final OfflineAuth auth; + private final List callSetIds, transcriptSetIds, variantAnnotationSetIds; + private final Map, String> refBaseCache; + + public AnnotateVariants(OfflineAuth auth, + List callSetIds, List transcriptSetIds, + List variantAnnotationSetIds) { + this.auth = auth; + this.callSetIds = callSetIds; + this.transcriptSetIds = transcriptSetIds; + this.variantAnnotationSetIds = variantAnnotationSetIds; + refBaseCache = Maps.newHashMap(); + } + + @Override + public void processElement( + DoFn>.ProcessContext c) throws Exception { + Genomics genomics = GenomicsFactory.builder().build().fromOfflineAuth(auth); + + SearchVariantsRequest request = c.element(); + LOG.info("processing contig " + request); + Iterable varIter = FluentIterable + .from(Paginator.Variants.create(genomics, ShardBoundary.Requirement.STRICT).search( + request + // TODO: Variants-only retrieval is not well support currently. For now + // we parameterize by CallSet for performance. + .setCallSetIds(callSetIds) + .setPageSize(VARIANTS_PAGE_SIZE), + VARIANT_FIELDS)) + .filter(VariantUtils.IS_SNP); + if (!varIter.iterator().hasNext()) { + LOG.info("region has no variants, skipping"); + return; + } + + IntervalTree transcripts = retrieveTranscripts(genomics, request); + ListMultimap, Annotation> variantAnnotations = + retrieveVariantAnnotations(genomics, request); + + Stopwatch stopwatch = Stopwatch.createStarted(); + int varCount = 0; + for (Variant variant : varIter) { + List alleles = ImmutableList.builder() + .addAll(variant.getAlternateBases()) + .add(variant.getReferenceBases()) + .build(); + Range pos = Range.openClosed(variant.getStart(), variant.getEnd()); + for (String allele : alleles) { + String outKey = Joiner.on(":").join( + variant.getReferenceName(), variant.getStart(), allele, variant.getId()); + for (Annotation match : variantAnnotations.get(pos)) { + if (allele.equals(match.getVariant().getAlternateBases())) { + // Exact match to a known variant annotation; straightforward join. + c.output(KV.of(outKey, match.getVariant())); + } + } + + Iterator> transcriptIter = transcripts.overlappers( + pos.lowerEndpoint().intValue(), pos.upperEndpoint().intValue() - 1); // Inclusive. + while (transcriptIter.hasNext()) { + // Calculate an effect of this allele on the coding region of the given transcript. + Annotation transcript = transcriptIter.next().getValue(); + VariantEffect effect = AnnotationUtils.determineVariantTranscriptEffect( + variant.getStart(), allele, transcript, + getCachedTranscriptBases(genomics, transcript)); + if (effect != null && !VariantEffect.SYNONYMOUS_SNP.equals(effect)) { + c.output(KV.of(outKey, new VariantAnnotation() + .setAlternateBases(allele) + .setType("SNP") + .setEffect(effect.toString()) + .setGeneId(transcript.getTranscript().getGeneId()) + .setTranscriptIds(ImmutableList.of(transcript.getId())))); + } + } + } + varCount++; + if (varCount%1e3 == 0) { + LOG.info(String.format("read %d variants (%.2f / s)", + varCount, (double)varCount / stopwatch.elapsed(TimeUnit.SECONDS))); + } + } + LOG.info("finished reading " + varCount + " variants in " + stopwatch); + } + + private ListMultimap, Annotation> retrieveVariantAnnotations( + Genomics genomics, SearchVariantsRequest request) { + Stopwatch stopwatch = Stopwatch.createStarted(); + ListMultimap, Annotation> annotationMap = ArrayListMultimap.create(); + Iterable annotationIter = + Paginator.Annotations.create(genomics, ShardBoundary.Requirement.OVERLAPS).search( + new SearchAnnotationsRequest() + .setAnnotationSetIds(variantAnnotationSetIds) + .setRange(new QueryRange() + .setReferenceName(canonicalizeRefName(request.getReferenceName())) + .setStart(request.getStart()) + .setEnd(request.getEnd()))); + for (Annotation annotation : annotationIter) { + RangePosition pos = annotation.getPosition(); + long start = 0; + if (pos.getStart() != null) { + start = pos.getStart(); + } + annotationMap.put(Range.closedOpen(start, pos.getEnd()), annotation); + } + LOG.info(String.format("read %d variant annotations in %s (%.2f / s)", annotationMap.size(), + stopwatch, (double)annotationMap.size() / stopwatch.elapsed(TimeUnit.SECONDS))); + return annotationMap; + } + + private IntervalTree retrieveTranscripts(Genomics genomics, SearchVariantsRequest request) { + Stopwatch stopwatch = Stopwatch.createStarted(); + IntervalTree transcripts = new IntervalTree<>(); + Iterable transcriptIter = + Paginator.Annotations.create(genomics, ShardBoundary.Requirement.OVERLAPS).search( + new SearchAnnotationsRequest() + .setAnnotationSetIds(transcriptSetIds) + .setRange(new QueryRange() + .setReferenceName(canonicalizeRefName(request.getReferenceName())) + .setStart(request.getStart()) + .setEnd(request.getEnd()))); + for (Annotation annotation : transcriptIter) { + RangePosition pos = annotation.getPosition(); + transcripts.put(pos.getStart().intValue(), pos.getEnd().intValue(), annotation); + } + LOG.info(String.format("read %d transcripts in %s (%.2f / s)", transcripts.size(), + stopwatch, (double)transcripts.size() / stopwatch.elapsed(TimeUnit.SECONDS))); + return transcripts; + } + + private String getCachedTranscriptBases(Genomics genomics, Annotation transcript) + throws IOException { + RangePosition pos = transcript.getPosition(); + Range rng = Range.closedOpen(pos.getStart(), pos.getEnd()); + if (!refBaseCache.containsKey(rng)) { + refBaseCache.put(rng, retrieveReferenceBases(genomics, pos)); + } + return refBaseCache.get(rng); + } + + private String retrieveReferenceBases(Genomics genomics, RangePosition pos) throws IOException { + StringBuilder b = new StringBuilder(); + String pageToken = ""; + while (true) { + // TODO: Support full request parameterization for Paginator.References.Bases. + ListBasesResponse response = genomics.references().bases() + .list(pos.getReferenceId()) + .setStart(pos.getStart()) + .setEnd(pos.getEnd()) + .setPageToken(pageToken) + .execute(); + b.append(response.getSequence()); + pageToken = response.getNextPageToken(); + if (Strings.isNullOrEmpty(pageToken)) { + break; + } + } + return b.toString(); + } + + private static String canonicalizeRefName(String refName) { + return refName.replace("chr", ""); + } + + public static void main(String[] args) throws Exception { + // Register the options so that they show up via --help + PipelineOptionsFactory.register(Options.class); + Options options = PipelineOptionsFactory.fromArgs(args) + .withValidation().as(Options.class); + // Option validation is not yet automatic, we make an explicit call here. + Options.Methods.validateOptions(options); + + OfflineAuth auth = GenomicsOptions.Methods.getGenomicsAuth(options); + Genomics genomics = GenomicsFactory.builder().build().fromOfflineAuth(auth); + + List callSetIds = ImmutableList.of(); + if (!Strings.isNullOrEmpty(options.getCallSetIds().trim())) { + callSetIds = ImmutableList.copyOf(options.getCallSetIds().split(",")); + } + List transcriptSetIds = + validateAnnotationSetsFlag(genomics, options.getTranscriptSetIds(), "TRANSCRIPT"); + List variantAnnotationSetIds = + validateAnnotationSetsFlag(genomics, options.getVariantAnnotationSetIds(), "VARIANT"); + validateRefsetForAnnotationSets(genomics, transcriptSetIds); + + List requests = options.isAllReferences() ? + ShardUtils.getPaginatedVariantRequests(options.getVariantSetId(), ShardUtils.SexChromosomeFilter.EXCLUDE_XY, + options.getBasesPerShard(), auth) : + ShardUtils.getPaginatedVariantRequests(options.getVariantSetId(), options.getReferences(), options.getBasesPerShard()); + + Pipeline p = Pipeline.create(options); + p.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + + p.begin() + .apply(Create.of(requests)) + .apply(ParDo.of(new AnnotateVariants(auth, callSetIds, transcriptSetIds, variantAnnotationSetIds))) + .apply(GroupByKey.create()) + .apply(ParDo.of(new DoFn>, String>() { + @Override + public void processElement(ProcessContext c) { + c.output(c.element().getKey() + ": " + c.element().getValue()); + } + })) + .apply(TextIO.Write.to(options.getOutput())); + p.run(); + } + + private static void validateRefsetForAnnotationSets( + Genomics genomics, List annosetIds) throws IOException { + String refsetId = null; + for (String annosetId : annosetIds) { + String gotId = genomics.annotationSets().get(annosetId).execute().getReferenceSetId(); + if (refsetId == null) { + refsetId = gotId; + } else if (!refsetId.equals(gotId)) { + throw new IllegalArgumentException("want consistent reference sets across the provided " + + "annotation sets, got " + refsetId + " and " + gotId); + } + } + } + + private static List validateAnnotationSetsFlag( + Genomics genomics, String flagValue, String wantType) throws IOException { + List annosetIds = ImmutableList.copyOf(flagValue.split(",")); + for (String annosetId : annosetIds) { + AnnotationSet annoset = genomics.annotationSets().get(annosetId).execute(); + if (!wantType.equals(annoset.getType())) { + throw new IllegalArgumentException("annotation set " + annosetId + " has type " + + annoset.getType() + ", wanted type " + wantType); + } + } + return annosetIds; + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/CalculateCoverage.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/CalculateCoverage.java new file mode 100644 index 0000000..a1e8596 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/CalculateCoverage.java @@ -0,0 +1,480 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import java.io.IOException; +import java.security.GeneralSecurityException; +import java.util.HashMap; +import java.util.List; + +import com.google.api.client.util.Strings; +import com.google.api.services.genomics.Genomics; +import com.google.api.services.genomics.model.Annotation; +import com.google.api.services.genomics.model.AnnotationSet; +import com.google.api.services.genomics.model.BatchCreateAnnotationsRequest; +import com.google.api.services.genomics.model.Position; +import com.google.api.services.genomics.model.RangePosition; +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.Description; +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.dataflow.sdk.options.Validation; +import com.google.cloud.dataflow.sdk.transforms.ApproximateQuantiles; +import com.google.cloud.dataflow.sdk.transforms.Combine; +import com.google.cloud.dataflow.sdk.transforms.Create; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.GroupByKey; +import com.google.cloud.dataflow.sdk.transforms.PTransform; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.transforms.SerializableFunction; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import com.google.cloud.genomics.dataflow.model.PosRgsMq; +import com.google.cloud.genomics.dataflow.readers.ReadGroupStreamer; +import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; +import com.google.cloud.genomics.dataflow.utils.ShardOptions; +import com.google.cloud.genomics.utils.Contig; +import com.google.cloud.genomics.utils.GenomicsFactory; +import com.google.cloud.genomics.utils.GenomicsUtils; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.cloud.genomics.utils.RetryPolicy; +import com.google.cloud.genomics.utils.ShardBoundary; +import com.google.cloud.genomics.utils.ShardUtils.SexChromosomeFilter; +import com.google.common.collect.Lists; +import com.google.genomics.v1.CigarUnit; +import com.google.genomics.v1.Read; + +/** + * Class for calculating read depth coverage for a given data set. + * + * For each "bucket" in the given input references, this computes the average coverage (rounded to + * six decimal places) across the bucket that 10%, 20%, 30%, etc. of the input ReadGroupsSets have + * for each mapping quality of the reads (<10:Low(L), 10-29:Medium(M), >=30:High(H)) as well as + * these same percentiles of ReadGroupSets for all reads regardless of mapping quality (Mapping + * quality All(A)). + * + * There is also the option to change the number of quantiles accordingly (numQuantiles = 5 would + * give you the minimum ReadGroupSet mean coverage for each and across all mapping qualities, the + * 25th, 50th, and 75th percentiles, and the maximum of these values). + * + * See + * http://googlegenomics.readthedocs.org/en/latest/use_cases/analyze_reads/calculate_coverage.html + * for running instructions. + */ +public class CalculateCoverage { + + /** + * Options required to run this pipeline. + * + * When specifying references, if you specify a nonzero starting point for any given reference, + * reads that start before that reference, even if they overlap with the reference, will NOT be + * counted. + */ + public static interface Options extends ShardOptions { + + @Description("A comma delimited list of the IDs of the Google Genomics ReadGroupSets this " + + "pipeline is working with. Default (empty) indicates all ReadGroupSets in InputDatasetId." + + " This or InputDatasetId must be set. InputDatasetId overrides ReadGroupSetIds " + + "(if InputDatasetId is set, this field will be ignored). All of the referenceSetIds for" + + " all ReadGroupSets in this list must be the same for the purposes of setting the" + + " referenceSetId of the output AnnotationSet.") + @Default.String("") + String getReadGroupSetIds(); + + void setReadGroupSetIds(String readGroupSetId); + + @Description("The ID of the Google Genomics Dataset that the pipeline will get its input reads" + + " from. Default (empty) means to use ReadGroupSetIds instead. This or ReadGroupSetIds" + + " must be set. InputDatasetId overrides ReadGroupSetIds (if this field is set, " + + "ReadGroupSetIds will be ignored). All of the referenceSetIds for all ReadGroupSets in" + + " this Dataset must be the same for the purposes of setting the referenceSetId" + + " of the output AnnotationSet.") + @Default.String("") + String getInputDatasetId(); + + void setInputDatasetId(String inputDatasetId); + + @Validation.Required + @Description("The ID of the Google Genomics Dataset that the output AnnotationSet will be " + + "posted to.") + @Default.String("") + String getOutputDatasetId(); + + void setOutputDatasetId(String outputDatasetId); + + @Description("The bucket width you would like to calculate coverage for. Default is 2048. " + + "Buckets are non-overlapping. If bucket width does not divide into the reference " + + "size, then the remainder will be a smaller bucket at the end of the reference.") + @Default.Integer(2048) + int getBucketWidth(); + + void setBucketWidth(int bucketWidth); + + @Description("The number of quantiles you would like to calculate for in the output. Default" + + "is 11 (minimum value for a particular grouping, 10-90 percentiles, and the maximum" + + " value). The InputDataset or list of ReadGroupSetIds specified must have an amount of " + + "ReadGroupSetIds greater than or equal to the number of quantiles that you are asking " + + "for.") + @Default.Integer(11) + int getNumQuantiles(); + + void setNumQuantiles(int numQuantiles); + } + + private static Options options; + private static Pipeline p; + private static OfflineAuth auth; + + public static void main(String[] args) throws GeneralSecurityException, IOException { + // Register the options so that they show up via --help + PipelineOptionsFactory.register(Options.class); + options = PipelineOptionsFactory.fromArgs(args).withValidation().as(Options.class); + + auth = GenomicsOptions.Methods.getGenomicsAuth(options); + + p = Pipeline.create(options); + p.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + + if (options.getInputDatasetId().isEmpty() && options.getReadGroupSetIds().isEmpty()) { + throw new IllegalArgumentException("InputDatasetId or ReadGroupSetIds must be specified"); + } + + List rgsIds; + if (options.getInputDatasetId().isEmpty()) { + rgsIds = Lists.newArrayList(options.getReadGroupSetIds().split(",")); + } else { + rgsIds = GenomicsUtils.getReadGroupSetIds(options.getInputDatasetId(), auth); + } + + if (rgsIds.size() < options.getNumQuantiles()) { + throw new IllegalArgumentException("Number of ReadGroupSets must be greater than or equal to" + + " the number of requested quantiles."); + } + + // Grab one ReferenceSetId to be used within the pipeline to confirm that all ReadGroupSets + // are associated with the same ReferenceSet. + String referenceSetId = GenomicsUtils.getReferenceSetId(rgsIds.get(0), auth); + if (Strings.isNullOrEmpty(referenceSetId)) { + throw new IllegalArgumentException("No ReferenceSetId associated with ReadGroupSetId " + + rgsIds.get(0) + + ". All ReadGroupSets in given input must have an associated ReferenceSet."); + } + + // Create our destination AnnotationSet for the associated ReferenceSet. + AnnotationSet annotationSet = createAnnotationSet(referenceSetId); + + PCollection reads = p.begin() + .apply(Create.of(rgsIds)) + .apply(ParDo.of(new CheckMatchingReferenceSet(referenceSetId, auth))) + .apply(new ReadGroupStreamer(auth, ShardBoundary.Requirement.STRICT, null, SexChromosomeFilter.INCLUDE_XY)); + + PCollection> coverageMeans = reads.apply(new CalculateCoverageMean()); + PCollection>>> quantiles + = coverageMeans.apply(new CalculateQuantiles(options.getNumQuantiles())); + PCollection>>>> answer = + quantiles.apply(GroupByKey.>>create()); + answer.apply(ParDo.of(new CreateAnnotations(annotationSet.getId(), auth, true))); + + p.run(); + } + + static class CheckMatchingReferenceSet extends DoFn { + private final String referenceSetIdForAllReadGroupSets; + private final OfflineAuth auth; + + public CheckMatchingReferenceSet(String referenceSetIdForAllReadGroupSets, + OfflineAuth auth) { + this.referenceSetIdForAllReadGroupSets = referenceSetIdForAllReadGroupSets; + this.auth = auth; + } + + @Override + public void processElement(DoFn.ProcessContext c) throws Exception { + String readGroupSetId = c.element(); + String referenceSetId = GenomicsUtils.getReferenceSetId(readGroupSetId, auth); + if (Strings.isNullOrEmpty(referenceSetId)) { + throw new IllegalArgumentException("No ReferenceSetId associated with ReadGroupSetId " + + readGroupSetId + + ". All ReadGroupSets in given input must have an associated ReferenceSet."); + } + if (!referenceSetIdForAllReadGroupSets.equals(referenceSetId)) { + throw new IllegalArgumentException("ReadGroupSets in given input must all be associated with" + + " the same ReferenceSetId : " + referenceSetId); + } + c.output(readGroupSetId); + } + } + + /** + * Composite PTransform that takes in Reads read in from various ReadGroupSetIds using the + * Genomics API and calculates the coverage mean at every distinct PosRgsMq object for the data + * input (Position, ReadgroupSetId, and Mapping Quality). + */ + public static class CalculateCoverageMean extends PTransform, + PCollection>> { + + @Override + public PCollection> apply(PCollection input) { + return input.apply(ParDo.of(new CoverageCounts())) + .apply(Combine.perKey(new SumCounts())) + .apply(ParDo.of(new CoverageMeans())); + } + } + + static class CoverageCounts extends DoFn> { + + private static final int LOW_MQ = 10; + private static final int HIGH_MQ = 30; + + @Override + public void processElement(ProcessContext c) { + if (c.element().getAlignment() != null) { //is mapped + // Calculate length of read + long readLength = 0; + for (CigarUnit cigar : c.element().getAlignment().getCigarList()) { + switch (cigar.getOperation()) { + case ALIGNMENT_MATCH: + case SEQUENCE_MATCH: + case SEQUENCE_MISMATCH: + case PAD: + case DELETE: + case SKIP: + readLength += cigar.getOperationLength(); + break; + } + } + // Get options for getting references/bucket width + Options pOptions = c.getPipelineOptions().as(Options.class); + // Calculate readEnd by shifting readStart by readLength + long readStart = c.element().getAlignment().getPosition().getPosition(); + long readEnd = readStart + readLength; + // Get starting and ending references + long refStart = 0; + long refEnd = Long.MAX_VALUE; + if (!pOptions.isAllReferences()) { + // If we aren't using all references, parse the references to get proper start and end + Iterable contigs = Contig.parseContigsFromCommandLine(pOptions.getReferences()); + for (Contig ct : contigs) { + if (ct.referenceName + .equals(c.element().getAlignment().getPosition().getReferenceName())) { + refStart = ct.start; + refEnd = ct.end; + } + } + } + // Calculate the index of the first bucket this read falls into + long bucket = ((readStart - refStart) + / pOptions.getBucketWidth()) * pOptions.getBucketWidth() + refStart; + long readCurr = readStart; + if (readStart < refStart) { + // If the read starts before the first bucket, start our calculations at the start of + // the reference, since we know the read has to overlap there or else it wouldn't + // be in our data set. + bucket = refStart; + readCurr = refStart; + } + while (readCurr < readEnd && readCurr < refEnd) { + // Loop over read to generate output for each bucket + long baseCount = 0; + long dist = Math.min(bucket + pOptions.getBucketWidth(), readEnd) - readCurr; + readCurr += dist; + baseCount += dist; + Position position = new Position() + .setPosition(bucket) + .setReferenceName(c.element().getAlignment().getPosition().getReferenceName()); + Integer mq = c.element().getAlignment().getMappingQuality(); + if (mq == null) { + mq = 0; + } + PosRgsMq.MappingQuality mqEnum; + if (mq < LOW_MQ) { + mqEnum = PosRgsMq.MappingQuality.L; + } else if (mq >= LOW_MQ && mq < HIGH_MQ) { + mqEnum = PosRgsMq.MappingQuality.M; + } else { + mqEnum = PosRgsMq.MappingQuality.H; + } + c.output(KV.of(new PosRgsMq(position, c.element().getReadGroupSetId(), mqEnum), baseCount)); + c.output(KV.of(new PosRgsMq( + position, c.element().getReadGroupSetId(), PosRgsMq.MappingQuality.A), baseCount)); + bucket += pOptions.getBucketWidth(); + } + } + } + } + + static class SumCounts implements SerializableFunction, Long> { + + @Override + public Long apply(Iterable input) { + long ans = 0; + for (Long l : input) { + ans += l; + } + return ans; + } + } + + static class CoverageMeans extends DoFn, KV> { + + @Override + public void processElement(ProcessContext c) { + KV ans = KV.of(c.element().getKey(), + (double) c.element().getValue() + / (double) c.getPipelineOptions().as(Options.class).getBucketWidth()); + c.output(ans); + } + } + + /** + * Composite PTransform that takes in the KV representing the coverage mean for a distinct + * PosRgsMq object (Position, ReadgroupsetId, and Mapping Quality) and calculates the quantiles + * such that 10% of the ReadGroupSetIds at a given Position (bucket) and mapping quality + * have at least this much coverage, and the same for 20%, etc., all the way up until 90%. It puts + * this into a KV object that can later be used to create annotations of the results. + * + * The percentiles will change based on the number of quantiles specified (see class description). + */ + public static class CalculateQuantiles extends PTransform>, + PCollection>>>> { + + private final int numQuantiles; + + public CalculateQuantiles(int numQuantiles) { + this.numQuantiles = numQuantiles; + } + + @Override + public PCollection>>> apply( + PCollection> input) { + return input.apply(ParDo.of(new RemoveRgsId())) + .apply(ApproximateQuantiles + ., Double>perKey(numQuantiles)) + .apply(ParDo.of(new MoveMapping())); + } + } + + static class RemoveRgsId extends DoFn, + KV, Double>> { + + @Override + public void processElement(ProcessContext c) { + KV ans = KV.of(KV.of(c.element().getKey().getPos(), c.element().getKey().getMq()), + c.element().getValue()); + c.output(ans); + } + } + + static class MoveMapping extends DoFn, List>, + KV>>> { + + @Override + public void processElement(ProcessContext c) { + KV ans = KV.of(c.element().getKey().getKey(), + KV.of(c.element().getKey().getValue(), c.element().getValue())); + c.output(ans); + } + } + + /* + TODO: If a particular batchCreateAnnotations request fails more than 4 times and the bundle gets + retried by the dataflow pipeline, some annotations may be written multiple times. + */ + static class CreateAnnotations extends + DoFn>>>, Annotation> { + + private final String asId; + private final OfflineAuth auth; + private final List currAnnotations; + private final boolean write; + + public CreateAnnotations(String asId, OfflineAuth auth, boolean write) { + this.asId = asId; + this.auth = auth; + this.currAnnotations = Lists.newArrayList(); + this.write = write; + } + + @Override + public void processElement(ProcessContext c) throws GeneralSecurityException, IOException { + Options pOptions = c.getPipelineOptions().as(Options.class); + Position bucket = c.element().getKey(); + Annotation a = new Annotation() + .setAnnotationSetId(asId) + .setPosition(new RangePosition() + .setStart(bucket.getPosition()) + .setEnd(bucket.getPosition() + pOptions.getBucketWidth()) + .setReferenceName(bucket.getReferenceName())) + .setType("GENERIC") + .setInfo(new HashMap>()); + for (KV> mappingQualityKV : c.element().getValue()) { + List output = Lists.newArrayList(); + for (int i = 0; i < mappingQualityKV.getValue().size(); i++) { + double value = Math.round(mappingQualityKV.getValue().get(i) * 1000000.0) / 1000000.0; + output.add(Double.toString(value)); + } + a.getInfo().put(mappingQualityKV.getKey().toString(), output); + } + if (write) { + currAnnotations.add(a); + if (currAnnotations.size() == 4096) { + // Batch create annotations once we hit the max amount for a batch + batchCreateAnnotations(); + } + } + c.output(a); + } + + @Override + public void finishBundle(Context c) throws IOException, GeneralSecurityException { + // Finish up any leftover annotations at the end. + if (write && !currAnnotations.isEmpty()) { + batchCreateAnnotations(); + } + } + + private void batchCreateAnnotations() throws IOException, GeneralSecurityException { + Genomics genomics = GenomicsFactory.builder().build().fromOfflineAuth(auth); + Genomics.Annotations.BatchCreate aRequest = genomics.annotations().batchCreate( + new BatchCreateAnnotationsRequest().setAnnotations(currAnnotations)); + RetryPolicy retryP = RetryPolicy.nAttempts(4); + retryP.execute(aRequest); + currAnnotations.clear(); + } + } + + private static AnnotationSet createAnnotationSet(String referenceSetId) + throws GeneralSecurityException, IOException { + if (referenceSetId == null) { + throw new IOException("ReferenceSetId was null for this readgroupset"); + } + // Create a new annotation set using the given datasetId, or the one that this data was from if + // one was not provided + AnnotationSet as = new AnnotationSet(); + as.setDatasetId(options.getOutputDatasetId()); + + if (!options.isAllReferences()) { + as.setName("Read Depth for " + options.getReferences()); + } else { + as.setName("Read Depth for all references"); + } + as.setReferenceSetId(referenceSetId); + as.setType("GENERIC"); + Genomics genomics = GenomicsFactory.builder().build().fromOfflineAuth(auth); + Genomics.AnnotationSets.Create asRequest = genomics.annotationSets().create(as); + AnnotationSet asWithId = asRequest.execute(); + return asWithId; + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/CountReads.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/CountReads.java new file mode 100644 index 0000000..dcf3ed1 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/CountReads.java @@ -0,0 +1,218 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import htsjdk.samtools.ValidationStringency; + +import java.io.IOException; +import java.math.BigInteger; +import java.security.GeneralSecurityException; +import java.util.Collections; +import java.util.List; +import java.util.logging.Logger; + +import com.google.api.services.genomics.model.Read; +import com.google.api.services.genomics.model.SearchReadsRequest; +import com.google.api.services.storage.Storage; +import com.google.api.services.storage.model.StorageObject; +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.io.TextIO; +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.Description; +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.dataflow.sdk.transforms.Count; +import com.google.cloud.dataflow.sdk.transforms.Create; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.util.gcsfs.GcsPath; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import com.google.cloud.genomics.dataflow.readers.ReadReader; +import com.google.cloud.genomics.dataflow.readers.bam.ReadBAMTransform; +import com.google.cloud.genomics.dataflow.readers.bam.Reader; +import com.google.cloud.genomics.dataflow.readers.bam.ReaderOptions; +import com.google.cloud.genomics.dataflow.readers.bam.ShardingPolicy; +import com.google.cloud.genomics.dataflow.utils.GCSOptions; +import com.google.cloud.genomics.dataflow.utils.GCSOutputOptions; +import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; +import com.google.cloud.genomics.dataflow.utils.ShardOptions; +import com.google.cloud.genomics.utils.Contig; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.cloud.genomics.utils.ShardBoundary; +import com.google.cloud.genomics.utils.ShardUtils; +import com.google.common.base.Strings; + +/** + * Simple read counting pipeline, intended as an example for reading data from + * APIs OR BAM files and invoking GATK tools. + * + * See http://googlegenomics.readthedocs.org/en/latest/use_cases/analyze_reads/count_reads.html + * for running instructions. + */ +public class CountReads { + + public static interface Options extends GCSOptions, ShardOptions, GCSOutputOptions { + + @Description("The ID of the Google Genomics ReadGroupSet this pipeline is working with. " + + "Default (empty) indicates all ReadGroupSets.") + @Default.String("") + String getReadGroupSetId(); + + void setReadGroupSetId(String readGroupSetId); + + @Description("The Google Cloud Storage path to the BAM file to get reads data from, if not using ReadGroupSet.") + @Default.String("") + String getBAMFilePath(); + + void setBAMFilePath(String filePath); + + @Description("Whether to shard BAM file reading.") + @Default.Boolean(true) + boolean isShardBAMReading(); + + void setShardBAMReading(boolean newValue); + + @Description("Whether to include unmapped mate pairs of mapped reads to match expectations of Picard tools.") + @Default.Boolean(false) + boolean isIncludeUnmapped(); + + void setIncludeUnmapped(boolean newValue); + + public static class Methods { + public static void validateOptions(Options options) { + GCSOutputOptions.Methods.validateOptions(options); + } + } + + } + + private static final Logger LOG = Logger.getLogger(CountReads.class.getName()); + private static Pipeline p; + private static Options pipelineOptions; + private static OfflineAuth auth; + + public static void main(String[] args) throws GeneralSecurityException, IOException { + // Register the options so that they show up via --help + PipelineOptionsFactory.register(Options.class); + pipelineOptions = PipelineOptionsFactory.fromArgs(args) + .withValidation().as(Options.class); + // Option validation is not yet automatic, we make an explicit call here. + Options.Methods.validateOptions(pipelineOptions); + + auth = GenomicsOptions.Methods.getGenomicsAuth(pipelineOptions); + p = Pipeline.create(pipelineOptions); + p.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + + // ensure data is accessible + String BAMFilePath = pipelineOptions.getBAMFilePath(); + if (!Strings.isNullOrEmpty(BAMFilePath)) { + if (GCSURLExists(BAMFilePath)) { + System.out.println(BAMFilePath + " is present, good."); + } else { + System.out.println("Error: " + BAMFilePath + " not found."); + return; + } + if (pipelineOptions.isShardBAMReading()) { + // the BAM code expects an index at BAMFilePath+".bai" + // and sharded reading will fail if the index isn't there. + String BAMIndexPath = BAMFilePath + ".bai"; + if (GCSURLExists(BAMIndexPath)) { + System.out.println(BAMIndexPath + " is present, good."); + } else { + System.out.println("Error: " + BAMIndexPath + " not found."); + return; + } + } + } + System.out.println("Output will be written to "+pipelineOptions.getOutput()); + + PCollection reads = getReads(); + PCollection readCount = reads.apply(Count.globally()); + PCollection readCountText = readCount.apply(ParDo.of(new DoFn() { + @Override + public void processElement(DoFn.ProcessContext c) throws Exception { + c.output(String.valueOf(c.element())); + } + }).named("toString")); + readCountText.apply(TextIO.Write.to(pipelineOptions.getOutput()).named("WriteOutput").withoutSharding()); + + p.run(); + } + + private static boolean GCSURLExists(String url) { + // ensure data is accessible + try { + // if we can read the size, then surely we can read the file + GcsPath fn = GcsPath.fromUri(url); + Storage.Objects storageClient = GCSOptions.Methods.createStorageClient(pipelineOptions, auth); + Storage.Objects.Get getter = storageClient.get(fn.getBucket(), fn.getObject()); + StorageObject object = getter.execute(); + BigInteger size = object.getSize(); + return true; + } catch (Exception x) { + return false; + } + } + + private static PCollection getReads() throws IOException { + if (!pipelineOptions.getBAMFilePath().isEmpty()) { + return getReadsFromBAMFile(); + } + if (!pipelineOptions.getReadGroupSetId().isEmpty()) { + return getReadsFromAPI(); + } + throw new IOException("Either BAM file or ReadGroupSet must be specified"); + } + + private static PCollection getReadsFromAPI() { + List requests = + ShardUtils.getPaginatedReadRequests(Collections.singletonList(pipelineOptions.getReadGroupSetId()), + pipelineOptions.getReferences(), pipelineOptions.getBasesPerShard()); + PCollection readRequests = p.begin() + .apply(Create.of(requests)); + PCollection reads = + readRequests.apply( + ParDo.of( + new ReadReader(auth, ShardBoundary.Requirement.STRICT)) + .named(ReadReader.class.getSimpleName())); + return reads; + } + + private static PCollection getReadsFromBAMFile() throws IOException { + LOG.info("getReadsFromBAMFile"); + + final Iterable contigs = Contig.parseContigsFromCommandLine(pipelineOptions.getReferences()); + final ReaderOptions readerOptions = new ReaderOptions( + ValidationStringency.LENIENT, + pipelineOptions.isIncludeUnmapped()); + if (pipelineOptions.isShardBAMReading()) { + LOG.info("Sharded reading of "+ pipelineOptions.getBAMFilePath()); + return ReadBAMTransform.getReadsFromBAMFilesSharded(p, + auth, + contigs, + readerOptions, + pipelineOptions.getBAMFilePath(), + ShardingPolicy.BYTE_SIZE_POLICY); + } else { // For testing and comparing sharded vs. not sharded only + LOG.info("Unsharded reading of " + pipelineOptions.getBAMFilePath()); + return p.apply( + Create.of( + Reader.readSequentiallyForTesting( + GCSOptions.Methods.createStorageClient(pipelineOptions, auth), + pipelineOptions.getBAMFilePath(), + contigs.iterator().next(), + readerOptions))); + } + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentityByState.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentityByState.java new file mode 100644 index 0000000..b2ab96a --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentityByState.java @@ -0,0 +1,128 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import java.util.List; + +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.io.TextIO; +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.Description; +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.dataflow.sdk.options.Validation; +import com.google.cloud.dataflow.sdk.transforms.Combine; +import com.google.cloud.dataflow.sdk.transforms.Create; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import com.google.cloud.genomics.dataflow.functions.AlleleSimilarityCalculator; +import com.google.cloud.genomics.dataflow.functions.CallSimilarityCalculatorFactory; +import com.google.cloud.genomics.dataflow.functions.FormatIBSData; +import com.google.cloud.genomics.dataflow.functions.IBSCalculator; +import com.google.cloud.genomics.dataflow.functions.SharedMinorAllelesCalculatorFactory; +import com.google.cloud.genomics.dataflow.functions.grpc.JoinNonVariantSegmentsWithVariants; +import com.google.cloud.genomics.dataflow.readers.VariantStreamer; +import com.google.cloud.genomics.dataflow.utils.GCSOutputOptions; +import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; +import com.google.cloud.genomics.dataflow.utils.ShardOptions; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.cloud.genomics.utils.ShardBoundary; +import com.google.cloud.genomics.utils.ShardUtils; +import com.google.genomics.v1.StreamVariantsRequest; +import com.google.genomics.v1.Variant; + +/** + * A pipeline that computes Identity by State (IBS) for each pair of individuals in a dataset. + * + * See http://googlegenomics.readthedocs.org/en/latest/use_cases/compute_identity_by_state/index.html + * for running instructions. + */ + +public class IdentityByState { + + public static interface Options extends ShardOptions, + JoinNonVariantSegmentsWithVariants.Options, GCSOutputOptions { + + @Description("The ID of the Google Genomics variant set this pipeline is accessing. " + + "Defaults to 1000 Genomes.") + @Default.String("10473108253681171589") + String getVariantSetId(); + + void setVariantSetId(String variantSetId); + + @Description("The class that determines the strategy for calculating the similarity of alleles.") + @Default.Class(SharedMinorAllelesCalculatorFactory.class) + Class getCallSimilarityCalculatorFactory(); + + void setCallSimilarityCalculatorFactory(Class kls); + + public static class Methods { + public static void validateOptions(Options options) { + JoinNonVariantSegmentsWithVariants.Options.Methods.validateOptions(options); + GCSOutputOptions.Methods.validateOptions(options); + } + } + + } + + // TODO: https://github.com/googlegenomics/utils-java/issues/48 + private static final String VARIANT_FIELDS = "variants(start,calls(genotype,callSetName))"; + + public static void main(String[] args) throws Exception { + // Register the options so that they show up via --help + PipelineOptionsFactory.register(Options.class); + Options options = + PipelineOptionsFactory.fromArgs(args).withValidation().as(Options.class); + // Option validation is not yet automatic, we make an explicit call here. + Options.Methods.validateOptions(options); + + OfflineAuth auth = GenomicsOptions.Methods.getGenomicsAuth(options); + List requests = options.isAllReferences() ? + ShardUtils.getVariantRequests(options.getVariantSetId(), ShardUtils.SexChromosomeFilter.EXCLUDE_XY, + options.getBasesPerShard(), auth) : + ShardUtils.getVariantRequests(options.getVariantSetId(), options.getReferences(), options.getBasesPerShard()); + + Pipeline p = Pipeline.create(options); + p.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + PCollection variants = p.begin() + .apply(Create.of(requests)) + .apply(new VariantStreamer(auth, ShardBoundary.Requirement.STRICT, VARIANT_FIELDS)); + + PCollection processedVariants; + if(options.getHasNonVariantSegments()) { + // Special handling is needed for data with non-variant segment records since IBS must + // take into account reference-matches in addition to the variants (unlike + // other analyses such as PCA). + processedVariants = JoinNonVariantSegmentsWithVariants.joinVariantsTransform(variants); + } else { + processedVariants = variants; + } + + processedVariants + .apply( + ParDo.named(AlleleSimilarityCalculator.class.getSimpleName()).of( + new AlleleSimilarityCalculator(getCallSimilarityCalculatorFactory(options)))) + .apply(Combine., KV>perKey(new IBSCalculator())) + .apply(ParDo.named(FormatIBSData.class.getSimpleName()).of(new FormatIBSData())) + .apply(TextIO.Write.named("WriteIBSData").to(options.getOutput())); + + p.run(); + } + + private static CallSimilarityCalculatorFactory getCallSimilarityCalculatorFactory( + Options options) throws InstantiationException, IllegalAccessException { + return options.getCallSimilarityCalculatorFactory().newInstance(); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java new file mode 100644 index 0000000..129002b --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java @@ -0,0 +1,233 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMRecordIterator; +import htsjdk.samtools.SamReader; +import htsjdk.samtools.ValidationStringency; + +import java.io.IOException; +import java.security.GeneralSecurityException; +import java.util.ArrayList; +import java.util.Collections; +import java.util.Comparator; +import java.util.logging.Logger; + +import com.google.api.services.genomics.model.Read; +import com.google.api.services.storage.Storage; +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.coders.Coder; +import com.google.cloud.dataflow.sdk.coders.DelegateCoder; +import com.google.cloud.dataflow.sdk.coders.StringUtf8Coder; +import com.google.cloud.dataflow.sdk.io.TextIO; +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.Description; +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.dataflow.sdk.util.Transport; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import com.google.cloud.genomics.dataflow.readers.bam.BAMIO; +import com.google.cloud.genomics.dataflow.readers.bam.ReadBAMTransform; +import com.google.cloud.genomics.dataflow.readers.bam.ReaderOptions; +import com.google.cloud.genomics.dataflow.readers.bam.ShardingPolicy; +import com.google.cloud.genomics.dataflow.utils.GCSOptions; +import com.google.cloud.genomics.dataflow.utils.GCSOutputOptions; +import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; +import com.google.cloud.genomics.dataflow.utils.ShardOptions; +import com.google.cloud.genomics.dataflow.utils.ShardReadsTransform; +import com.google.cloud.genomics.dataflow.writers.WriteReadsTransform; +import com.google.cloud.genomics.utils.Contig; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.common.collect.Lists; + +/** + * Demonstrates loading some Reads, sharding them, writing them to various BAM files in parallel, + * then combining the shards and writing an index for the combined BAM file. + */ +public class ShardedBAMWriting { + + static interface Options extends ShardOptions, ShardReadsTransform.Options, + WriteReadsTransform.Options, GCSOutputOptions { + @Description("The Google Cloud Storage path to the BAM file to get reads data from") + @Default.String("") + String getBAMFilePath(); + + void setBAMFilePath(String filePath); + + public static class Methods { + public static void validateOptions(Options options) { + GCSOutputOptions.Methods.validateOptions(options); + } + } + + } + + private static final Logger LOG = Logger.getLogger(ShardedBAMWriting.class.getName()); + private static final String BAM_INDEX_FILE_MIME_TYPE = "application/octet-stream"; + private static final int MAX_FILES_FOR_COMPOSE = 32; + private static Options pipelineOptions; + private static Pipeline pipeline; + private static OfflineAuth auth; + private static Iterable contigs; + + public static void main(String[] args) throws GeneralSecurityException, IOException { + // Register the options so that they show up via --help + PipelineOptionsFactory.register(Options.class); + pipelineOptions = PipelineOptionsFactory.fromArgs(args) + .withValidation().as(Options.class); + // Option validation is not yet automatic, we make an explicit call here. + Options.Methods.validateOptions(pipelineOptions); + + auth = GenomicsOptions.Methods.getGenomicsAuth(pipelineOptions); + pipeline = Pipeline.create(pipelineOptions); + // Register coders. + pipeline.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + pipeline.getCoderRegistry().registerCoder(Contig.class, CONTIG_CODER); + // Process options. + contigs = Contig.parseContigsFromCommandLine(pipelineOptions.getReferences()); + // Get header info. + final HeaderInfo headerInfo = getHeader(); + + // Get the reads and shard them. + final PCollection reads = getReadsFromBAMFile(); + final PCollection>> shardedReads = ShardReadsTransform.shard(reads); + final PCollection writtenShards = WriteReadsTransform.write( + shardedReads, headerInfo, pipelineOptions.getOutput(), pipeline); + writtenShards + .apply( + TextIO.Write + .to(pipelineOptions.getOutput() + "-result") + .named("Write Output Result") + .withoutSharding()); + pipeline.run(); + } + + public static class HeaderInfo { + public SAMFileHeader header; + public Contig firstShard; + + public HeaderInfo(SAMFileHeader header, Contig firstShard) { + this.header = header; + this.firstShard = firstShard; + } + } + + private static HeaderInfo getHeader() throws IOException { + HeaderInfo result = null; + + // Get first contig + final ArrayList contigsList = Lists.newArrayList(contigs); + if (contigsList.size() <= 0) { + throw new IOException("No contigs specified"); + } + Collections.sort(contigsList, new Comparator() { + @Override + public int compare(Contig o1, Contig o2) { + int compRefs = o1.referenceName.compareTo(o2.referenceName); + if (compRefs != 0) { + return compRefs; + } + return (int)(o1.start - o2.start); + } + }); + final Contig firstContig = contigsList.get(0); + + // Open and read start of BAM + final Storage.Objects storage = Transport.newStorageClient( + pipelineOptions + .as(GCSOptions.class)) + .build() + .objects(); + LOG.info("Reading header from " + pipelineOptions.getBAMFilePath()); + final SamReader samReader = BAMIO + .openBAM(storage, pipelineOptions.getBAMFilePath(), ValidationStringency.DEFAULT_STRINGENCY); + final SAMFileHeader header = samReader.getFileHeader(); + + LOG.info("Reading first chunk of reads from " + pipelineOptions.getBAMFilePath()); + final SAMRecordIterator recordIterator = samReader.query( + firstContig.referenceName, (int)firstContig.start + 1, (int)firstContig.end + 1, false); + + Contig firstShard = null; + while (recordIterator.hasNext() && result == null) { + SAMRecord record = recordIterator.next(); + final int alignmentStart = record.getAlignmentStart(); + if (firstShard == null && alignmentStart > firstContig.start && alignmentStart < firstContig.end) { + firstShard = shardFromAlignmentStart(firstContig.referenceName, alignmentStart, pipelineOptions.getLociPerWritingShard()); + LOG.info("Determined first shard to be " + firstShard); + result = new HeaderInfo(header, firstShard); + } + } + recordIterator.close(); + samReader.close(); + + if (result == null) { + throw new IOException("Did not find reads for the first contig " + firstContig.toString()); + } + LOG.info("Finished header reading from " + pipelineOptions.getBAMFilePath()); + return result; + } + + /** + * Policy used to shard Reads. + * By default we are using the default sharding supplied by the policy class. + * If you want custom sharding, use the following pattern: + * 
+   *    READ_SHARDING_POLICY = new ShardingPolicy() {
+   *     @Override
+   *     public boolean shardBigEnough(BAMShard shard) {
+   *       return shard.sizeInLoci() > 50000000;
+   *     }
+   *   };
+   *
+ */ + private static final ShardingPolicy READ_SHARDING_POLICY = ShardingPolicy.BYTE_SIZE_POLICY; + + private static PCollection getReadsFromBAMFile() throws IOException { + LOG.info("Sharded reading of "+ pipelineOptions.getBAMFilePath()); + + final ReaderOptions readerOptions = new ReaderOptions( + ValidationStringency.DEFAULT_STRINGENCY, + true); + + return ReadBAMTransform.getReadsFromBAMFilesSharded(pipeline, + auth, + contigs, + readerOptions, + pipelineOptions.getBAMFilePath(), + READ_SHARDING_POLICY); + } + + static Coder CONTIG_CODER = DelegateCoder.of( + StringUtf8Coder.of(), + new DelegateCoder.CodingFunction() { + @Override + public String apply(Contig contig) throws Exception { + return contig.toString(); + } + }, + new DelegateCoder.CodingFunction() { + @Override + public Contig apply(String str) throws Exception { + return Contig.parseContigsFromCommandLine(str).iterator().next(); + } + }); + + static Contig shardFromAlignmentStart(String referenceName, long alignmentStart, long lociPerShard) { + final long shardStart = (alignmentStart / lociPerShard) * lociPerShard; + return new Contig(referenceName, shardStart, shardStart + lociPerShard); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/TransmissionProbability.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/TransmissionProbability.java new file mode 100644 index 0000000..455068c --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/TransmissionProbability.java @@ -0,0 +1,125 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import java.io.IOException; +import java.security.GeneralSecurityException; +import java.util.List; + +import com.google.api.services.genomics.model.SearchVariantsRequest; +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.io.TextIO; +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.Description; +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.dataflow.sdk.transforms.Create; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.GroupByKey; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import com.google.cloud.genomics.dataflow.functions.CalculateTransmissionProbability; +import com.google.cloud.genomics.dataflow.functions.ExtractAlleleTransmissionStatus; +import com.google.cloud.genomics.dataflow.model.Allele; +import com.google.cloud.genomics.dataflow.readers.VariantReader; +import com.google.cloud.genomics.dataflow.utils.GCSOutputOptions; +import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; +import com.google.cloud.genomics.dataflow.utils.ShardOptions; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.cloud.genomics.utils.ShardBoundary; +import com.google.cloud.genomics.utils.ShardUtils; + +/** + * A pipeline that calculates the transmission probability of each allele in parents. + * See the README for running instructions. + */ +public class TransmissionProbability { + + public static interface Options extends ShardOptions, GCSOutputOptions { + + @Description("The ID of the Google Genomics variant set this pipeline is accessing. " + + "Defaults to 1000 Genomes.") + @Default.String("10473108253681171589") + String getVariantSetId(); + + void setVariantSetId(String variantSetId); + + @Description("Whether to use the gRPC API endpoint for variants. Defaults to 'true';") + @Default.Boolean(true) + Boolean getUseGrpc(); + + void setUseGrpc(Boolean value); + + public static class Methods { + public static void validateOptions(Options options) { + GCSOutputOptions.Methods.validateOptions(options); + } + } + + } + + // TODO https://github.com/googlegenomics/utils-java/issues/48 + private static final String VARIANT_FIELDS + = "nextPageToken,variants(id,start,names,calls(info,callSetName))"; + + public static void main(String[] args) throws IOException, GeneralSecurityException { + // Register the options so that they show up via --help + PipelineOptionsFactory.register(Options.class); + Options options = PipelineOptionsFactory.fromArgs(args) + .withValidation().as(Options.class); + // Option validation is not yet automatic, we make an explicit call here. + Options.Methods.validateOptions(options); + + OfflineAuth auth = GenomicsOptions.Methods.getGenomicsAuth(options); + List requests = options.isAllReferences() ? + ShardUtils.getPaginatedVariantRequests(options.getVariantSetId(), ShardUtils.SexChromosomeFilter.EXCLUDE_XY, + options.getBasesPerShard(), auth) : + ShardUtils.getPaginatedVariantRequests(options.getVariantSetId(), options.getReferences(), options.getBasesPerShard()); + + Pipeline p = Pipeline.create(options); + p.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + + // The below pipeline works as follows: + // - Fetch the variants, + // - For each Variant, see which alleles were actually transmitted to + // the child + // - Groups Transmission sources by Variant, + // - Calculate transmission Probability for each variant + // - Print calculated values to a file. + p.begin() + .apply(Create.of(requests)) + .apply(ParDo.named("VariantReader") + .of(new VariantReader(auth, ShardBoundary.Requirement.STRICT, VARIANT_FIELDS))) + .apply(ParDo.named("ExtractFamilyVariantStatus") + .of(new ExtractAlleleTransmissionStatus())) + .apply(GroupByKey.create()) + .apply(ParDo.named("CalculateTransmissionProbability") + .of(new CalculateTransmissionProbability())) + .apply(ParDo.named("WriteDataToFile") + .of(new DoFn, String>() { + @Override + public void processElement(ProcessContext c) { + KV pair = c.element(); + String output = pair.getKey().getReferenceName() + "\t" + + pair.getKey().getAllele() + "\t" + pair.getValue() + "\n"; + c.output(output); + } + })) + .apply(TextIO.Write.named("WriteResults").to(options.getOutput())); + + p.run(); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/VariantSimilarity.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/VariantSimilarity.java new file mode 100644 index 0000000..5c5fba6 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/VariantSimilarity.java @@ -0,0 +1,129 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import java.io.IOException; +import java.security.GeneralSecurityException; +import java.util.Collections; +import java.util.List; + +import com.google.api.services.genomics.model.SearchVariantsRequest; +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.Description; +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.dataflow.sdk.transforms.Create; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import com.google.cloud.genomics.dataflow.functions.ExtractSimilarCallsets; +import com.google.cloud.genomics.dataflow.functions.OutputPCoAFile; +import com.google.cloud.genomics.dataflow.readers.VariantReader; +import com.google.cloud.genomics.dataflow.readers.VariantStreamer; +import com.google.cloud.genomics.dataflow.utils.GCSOutputOptions; +import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; +import com.google.cloud.genomics.dataflow.utils.ShardOptions; +import com.google.cloud.genomics.utils.GenomicsUtils; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.cloud.genomics.utils.ShardBoundary; +import com.google.cloud.genomics.utils.ShardUtils; +import com.google.common.collect.BiMap; +import com.google.common.collect.HashBiMap; +import com.google.genomics.v1.StreamVariantsRequest; + +/** + * A pipeline that generates similarity data for variants in a dataset. + * + * See http://googlegenomics.readthedocs.org/en/latest/use_cases/compute_principal_coordinate_analysis/index.html + * for running instructions. + */ +public class VariantSimilarity { + + public static interface Options extends ShardOptions, GCSOutputOptions { + + @Description("The ID of the Google Genomics variant set this pipeline is accessing. " + + "Defaults to 1000 Genomes.") + @Default.String("10473108253681171589") + String getVariantSetId(); + + void setVariantSetId(String variantSetId); + + @Description("Whether to use the gRPC API endpoint for variants. Defaults to 'true';") + @Default.Boolean(true) + Boolean getUseGrpc(); + + void setUseGrpc(Boolean value); + + public static class Methods { + public static void validateOptions(Options options) { + GCSOutputOptions.Methods.validateOptions(options); + } + } + + } + + // TODO https://github.com/googlegenomics/utils-java/issues/48 + private static final String VARIANT_FIELDS = "nextPageToken,variants(start,calls(genotype,callSetName))"; + + public static void main(String[] args) throws IOException, GeneralSecurityException { + // Register the options so that they show up via --help + PipelineOptionsFactory.register(Options.class); + Options options = PipelineOptionsFactory.fromArgs(args) + .withValidation().as(Options.class); + // Option validation is not yet automatic, we make an explicit call here. + Options.Methods.validateOptions(options); + + OfflineAuth auth = GenomicsOptions.Methods.getGenomicsAuth(options); + + List callSetNames = GenomicsUtils.getCallSetsNames(options.getVariantSetId() , auth); + Collections.sort(callSetNames); // Ensure a stable sort order for reproducible results. + BiMap dataIndices = HashBiMap.create(); + for(String callSetName : callSetNames) { + dataIndices.put(callSetName, dataIndices.size()); + } + + Pipeline p = Pipeline.create(options); + + p.begin(); + PCollection, Long>> similarCallsets = null; + + if(options.getUseGrpc()) { + List requests = options.isAllReferences() ? + ShardUtils.getVariantRequests(options.getVariantSetId(), ShardUtils.SexChromosomeFilter.EXCLUDE_XY, + options.getBasesPerShard(), auth) : + ShardUtils.getVariantRequests(options.getVariantSetId(), options.getReferences(), options.getBasesPerShard()); + + similarCallsets = p.apply(Create.of(requests)) + .apply(new VariantStreamer(auth, ShardBoundary.Requirement.STRICT, VARIANT_FIELDS)) + .apply(ParDo.of(new ExtractSimilarCallsets.v1())); + } else { + p.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + List requests = options.isAllReferences() ? + ShardUtils.getPaginatedVariantRequests(options.getVariantSetId(), ShardUtils.SexChromosomeFilter.EXCLUDE_XY, + options.getBasesPerShard(), auth) : + ShardUtils.getPaginatedVariantRequests(options.getVariantSetId(), options.getReferences(), options.getBasesPerShard()); + + similarCallsets = p.apply(Create.of(requests)) + .apply(ParDo.of(new VariantReader(auth, ShardBoundary.Requirement.STRICT, VARIANT_FIELDS))) + .apply(ParDo.of(new ExtractSimilarCallsets.v1beta2())); + } + + similarCallsets.apply(new OutputPCoAFile(dataIndices, options.getOutput())); + + p.run(); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/VerifyBamId.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/VerifyBamId.java new file mode 100644 index 0000000..bf50f39 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/VerifyBamId.java @@ -0,0 +1,494 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import java.io.IOException; +import java.io.UnsupportedEncodingException; +import java.nio.ByteBuffer; +import java.security.GeneralSecurityException; +import java.security.MessageDigest; +import java.security.NoSuchAlgorithmException; +import java.util.Arrays; +import java.util.List; +import java.util.Map; + +import com.google.api.client.util.Strings; +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.io.TextIO; +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.Description; +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.dataflow.sdk.transforms.Create; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.Filter; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.transforms.SerializableFunction; +import com.google.cloud.dataflow.sdk.transforms.View; +import com.google.cloud.dataflow.sdk.transforms.join.CoGbkResult; +import com.google.cloud.dataflow.sdk.transforms.join.CoGroupByKey; +import com.google.cloud.dataflow.sdk.transforms.join.KeyedPCollectionTuple; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.dataflow.sdk.values.PCollectionView; +import com.google.cloud.dataflow.sdk.values.TupleTag; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import com.google.cloud.genomics.dataflow.functions.LikelihoodFn; +import com.google.cloud.genomics.dataflow.model.AlleleFreq; +import com.google.cloud.genomics.dataflow.model.ReadBaseQuality; +import com.google.cloud.genomics.dataflow.model.ReadBaseWithReference; +import com.google.cloud.genomics.dataflow.model.ReadCounts; +import com.google.cloud.genomics.dataflow.model.ReadQualityCount; +import com.google.cloud.genomics.dataflow.pipelines.CalculateCoverage.CheckMatchingReferenceSet; +import com.google.cloud.genomics.dataflow.readers.ReadGroupStreamer; +import com.google.cloud.genomics.dataflow.readers.VariantStreamer; +import com.google.cloud.genomics.dataflow.utils.GCSOutputOptions; +import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; +import com.google.cloud.genomics.dataflow.utils.ReadFunctions; +import com.google.cloud.genomics.dataflow.utils.ShardOptions; +import com.google.cloud.genomics.dataflow.utils.Solver; +import com.google.cloud.genomics.dataflow.utils.VariantFunctions; +import com.google.cloud.genomics.utils.GenomicsUtils; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.cloud.genomics.utils.ShardBoundary; +import com.google.cloud.genomics.utils.ShardUtils; +import com.google.cloud.genomics.utils.ShardUtils.SexChromosomeFilter; +import com.google.common.collect.ImmutableMultiset; +import com.google.common.collect.Lists; +import com.google.common.collect.Multiset; +import com.google.genomics.v1.Position; +import com.google.genomics.v1.Read; +import com.google.genomics.v1.StreamVariantsRequest; +import com.google.genomics.v1.Variant; +import com.google.protobuf.ListValue; + +/** + * Test a set of reads for contamination. + * + * Takes a set of specified ReadGroupSets of reads to test and statistics on reference allele + * frequencies for SNPs with a single alternative from a specified set of VariantSets. + * + * See http://googlegenomics.readthedocs.org/en/latest/use_cases/perform_quality_control_checks/verify_bam_id.html + * for running instructions. + * + * Uses the sequence data alone approach described in: + * G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, + * G. Abecasis, M. Boehnke,and H. M. Kang, Detecting and Estimating + * Contamination of Human DNA Samples in Sequencing and Array-Based Genotype + * Data, American journal of human genetics doi:10.1016/j.ajhg.2012.09.004 + * (volume 91 issue 5 pp.839 - 848) + * http://www.sciencedirect.com/science/article/pii/S0002929712004788 + */ +public class VerifyBamId { + + /** + * Options required to run this pipeline. + */ + public static interface Options extends ShardOptions, GCSOutputOptions { + + @Description("A comma delimited list of the IDs of the Google Genomics ReadGroupSets this " + + "pipeline is working with. Default (empty) indicates all ReadGroupSets in InputDatasetId." + + " This or InputDatasetId must be set. InputDatasetId overrides " + + "ReadGroupSetIds (if InputDatasetId is set, this field will be ignored).") + @Default.String("") + String getReadGroupSetIds(); + + void setReadGroupSetIds(String readGroupSetId); + + @Description("The ID of the Google Genomics Dataset that the pipeline will get its input reads" + + " from. Default (empty) means to use ReadGroupSetIds and VariantSetIds instead. This or" + + " ReadGroupSetIds and VariantSetIds must be set. InputDatasetId overrides" + + " ReadGroupSetIds and VariantSetIds (if this field is set, ReadGroupSetIds and" + + " VariantSetIds will be ignored).") + @Default.String("") + String getInputDatasetId(); + + void setInputDatasetId(String inputDatasetId); + + public String DEFAULT_VARIANTSET = "10473108253681171589"; + @Description("The ID of the Google Genomics VariantSet this pipeline is working with." + + " It assumes the variant set has INFO field 'AF' from which it retrieves the" + + " allele frequency for the variant, such as 1,000 Genomes phase 1 or phase 3 variants." + + " Defaults to the 1,000 Genomes phase 1 VariantSet with id " + DEFAULT_VARIANTSET + ".") + @Default.String(DEFAULT_VARIANTSET) + String getVariantSetId(); + + void setVariantSetId(String variantSetId); + + @Description("The minimum allele frequency to use in analysis. Defaults to 0.01.") + @Default.Double(0.01) + double getMinFrequency(); + + void setMinFrequency(double minFrequency); + + @Description("The fraction of positions to check. Defaults to 0.01.") + @Default.Double(0.01) + double getSamplingFraction(); + + void setSamplingFraction(double minFrequency); + + public static class Methods { + public static void validateOptions(Options options) { + GCSOutputOptions.Methods.validateOptions(options); + } + } + + } + + private static Pipeline p; + private static Options pipelineOptions; + private static OfflineAuth auth; + + /** + * String prefix used for sampling hash function + */ + private static final String HASH_PREFIX = ""; + + // TODO: this value is not quite correct. Test again after + // https://github.com/googlegenomics/utils-java/issues/48 + private static final String VARIANT_FIELDS = "variants(start,calls(genotype,callSetName))"; + + /** + * Run the VerifyBamId algorithm and output the resulting contamination estimate. + */ + public static void main(String[] args) throws GeneralSecurityException, IOException { + // Register the options so that they show up via --help + PipelineOptionsFactory.register(Options.class); + pipelineOptions = PipelineOptionsFactory.fromArgs(args) + .withValidation().as(Options.class); + // Option validation is not yet automatic, we make an explicit call here. + Options.Methods.validateOptions(pipelineOptions); + + auth = GenomicsOptions.Methods.getGenomicsAuth(pipelineOptions); + + p = Pipeline.create(pipelineOptions); + p.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + + if (pipelineOptions.getInputDatasetId().isEmpty() && pipelineOptions.getReadGroupSetIds().isEmpty()) { + throw new IllegalArgumentException("InputDatasetId or ReadGroupSetIds must be specified"); + } + + List rgsIds; + if (pipelineOptions.getInputDatasetId().isEmpty()) { + rgsIds = Lists.newArrayList(pipelineOptions.getReadGroupSetIds().split(",")); + } else { + rgsIds = GenomicsUtils.getReadGroupSetIds(pipelineOptions.getInputDatasetId(), auth); + } + + // Grab one ReferenceSetId to be used within the pipeline to confirm that all ReadGroupSets + // are associated with the same ReferenceSet. + String referenceSetId = GenomicsUtils.getReferenceSetId(rgsIds.get(0), auth); + if (Strings.isNullOrEmpty(referenceSetId)) { + throw new IllegalArgumentException("No ReferenceSetId associated with ReadGroupSetId " + + rgsIds.get(0) + + ". All ReadGroupSets in given input must have an associated ReferenceSet."); + } + + // TODO: confirm that variant set also corresponds to the same reference + // https://github.com/googlegenomics/api-client-java/issues/66 + + // Reads in Reads. + PCollection reads = p.begin() + .apply(Create.of(rgsIds)) + .apply(ParDo.of(new CheckMatchingReferenceSet(referenceSetId, auth))) + .apply(new ReadGroupStreamer(auth, ShardBoundary.Requirement.STRICT, null, SexChromosomeFilter.INCLUDE_XY)); + + /* + TODO: We can reduce the number of requests needed to be created by doing the following: + 1. Stream the Variants first (rather than concurrently with the Reads). Select a subset of + them equal to some threshold (say 50K by default). + 2. Create the requests for streaming Reads by running a ParDo over the selected Variants + to get their ranges (we only need to stream Reads that overlap the selected Variants). + 3. Stream the Reads from the created requests. + */ + + // Reads in Variants. TODO potentially provide an option to load the Variants from a file. + List variantRequests = pipelineOptions.isAllReferences() ? + ShardUtils.getVariantRequests(pipelineOptions.getVariantSetId(), ShardUtils.SexChromosomeFilter.INCLUDE_XY, + pipelineOptions.getBasesPerShard(), auth) : + ShardUtils.getVariantRequests(pipelineOptions.getVariantSetId(), pipelineOptions.getReferences(), pipelineOptions.getBasesPerShard()); + + PCollection variants = p.apply(Create.of(variantRequests)) + .apply(new VariantStreamer(auth, ShardBoundary.Requirement.STRICT, VARIANT_FIELDS)); + + PCollection> refFreq = getFreq(variants, pipelineOptions.getMinFrequency()); + + PCollection> readCountsTable = + combineReads(reads, pipelineOptions.getSamplingFraction(), HASH_PREFIX, refFreq); + + // Converts our results to a single Map of Position keys to ReadCounts values. + PCollectionView> view = readCountsTable + .apply(View.asMap()); + + // Calculates the contamination estimate based on the resulting Map above. + PCollection result = p.begin().apply(Create.of("")) + .apply(ParDo.of(new Maximizer(view)).withSideInputs(view)); + + // Writes the result to the given output location in Cloud Storage. + result.apply(TextIO.Write.to(pipelineOptions.getOutput()).named("WriteOutput").withoutSharding()); + + p.run(); + + } + + /** + * Compute a PCollection of reference allele frequencies for SNPs of interest. + * The SNPs all have only a single alternate allele, and neither the + * reference nor the alternate allele have a population frequency < minFreq. + * The results are returned in a PCollection indexed by Position. + * + * @param variants a set of variant calls for a reference population + * @param minFreq the minimum allele frequency for the set + * @return a PCollection mapping Position to AlleleCounts + */ + static PCollection> getFreq( + PCollection variants, double minFreq) { + return variants.apply(Filter.byPredicate(VariantFunctions.IS_PASSING).named("PassingFilter")) + .apply(Filter.byPredicate(VariantFunctions.IS_ON_CHROMOSOME).named("OnChromosomeFilter")) + .apply(Filter.byPredicate(VariantFunctions.IS_NOT_LOW_QUALITY).named("NotLowQualityFilter")) + .apply(Filter.byPredicate(VariantFunctions.IS_SINGLE_ALTERNATE_SNP).named("SNPFilter")) + .apply(ParDo.of(new GetAlleleFreq())) + .apply(Filter.byPredicate(new FilterFreq(minFreq))); + } + + /** + * Filter, pile up, and sample reads, then join against reference statistics. + * + * @param reads A PCollection of reads + * @param samplingFraction Fraction of reads to keep + * @param samplingPrefix A prefix used in generating hashes used in sampling + * @param refCounts A PCollection mapping position to counts of alleles in + * a reference population. + * @return A PCollection mapping Position to a ReadCounts proto + */ + static PCollection> combineReads(PCollection reads, + double samplingFraction, String samplingPrefix, + PCollection> refFreq) { + // Runs filters on input Reads, splits into individual aligned bases (emitting the + // base and quality) and grabs a sample of them based on a hash mod of Position. + PCollection> joinReadCounts = + reads.apply(Filter.byPredicate(ReadFunctions.IS_ON_CHROMOSOME).named("IsOnChromosome")) + .apply(Filter.byPredicate(ReadFunctions.IS_NOT_QC_FAILURE).named("IsNotQCFailure")) + .apply(Filter.byPredicate(ReadFunctions.IS_NOT_DUPLICATE).named("IsNotDuplicate")) + .apply(Filter.byPredicate(ReadFunctions.IS_PROPER_PLACEMENT).named("IsProperPlacement")) + .apply(ParDo.of(new SplitReads())) + .apply(Filter.byPredicate(new SampleReads(samplingFraction, samplingPrefix))); + + TupleTag readCountsTag = new TupleTag<>(); + TupleTag refFreqTag = new TupleTag<>(); + // Pile up read counts, then join against reference stats. + PCollection> joined = KeyedPCollectionTuple + .of(readCountsTag, joinReadCounts) + .and(refFreqTag, refFreq) + .apply(CoGroupByKey.create()); + return joined.apply(ParDo.of(new PileupAndJoinReads(readCountsTag, refFreqTag))); + } + + /** + * Split reads into individual aligned bases and emit base + quality. + */ + static class SplitReads extends DoFn> { + + @Override + public void processElement(ProcessContext c) throws Exception { + List readBases = ReadFunctions.extractReadBases(c.element()); + if (!readBases.isEmpty()) { + for (ReadBaseWithReference rb : readBases) { + c.output(KV.of(rb.getRefPosition(), rb.getRbq())); + } + } + } + } + + /** + * Sample bases via a hash mod of position. + */ + static class SampleReads implements SerializableFunction, Boolean> { + + private final double samplingFraction; + private final String samplingPrefix; + + public SampleReads(double samplingFraction, String samplingPrefix) { + this.samplingFraction = samplingFraction; + this.samplingPrefix = samplingPrefix; + } + + @Override + public Boolean apply(KV input) { + if (samplingFraction == 1.0) { + return true; + } else { + byte[] msg; + Position position = input.getKey(); + try { + msg = (samplingPrefix + position.getReferenceName() + ":" + position.getPosition() + ":" + + position.getReverseStrand()).getBytes("UTF-8"); + } catch (UnsupportedEncodingException e) { + throw new AssertionError("UTF-8 not available - should not happen"); + } + MessageDigest md; + try { + md = MessageDigest.getInstance("MD5"); + } catch (NoSuchAlgorithmException e) { + throw new AssertionError("MD5 not available - should not happen"); + } + byte[] digest = md.digest(msg); + if (digest.length != 16) { + throw new AssertionError("MD5 should return 128 bits"); + } + ByteBuffer buffer = ByteBuffer.allocate(Long.SIZE); + buffer.put(Arrays.copyOf(digest, Long.SIZE)); + return ((((double) buffer.getLong(0) / (double) ((long) 1 << 63)) + 1.0) * 0.5) + < samplingFraction; + } + } + } + + /** + * Map a variant to a Position, AlleleFreq pair. + */ + static class GetAlleleFreq extends DoFn> { + + @Override + public void processElement(ProcessContext c) throws Exception { + ListValue lv = c.element().getInfo().get("AF"); + if (lv != null && lv.getValuesCount() > 0) { + Position position = Position.newBuilder() + .setPosition(c.element().getStart()) + .setReferenceName(c.element().getReferenceName()) + .build(); + AlleleFreq af = new AlleleFreq(); + af.setRefFreq(lv.getValues(0).getNumberValue()); + af.setAltBases(c.element().getAlternateBasesList()); + af.setRefBases(c.element().getReferenceBases()); + c.output(KV.of(position, af)); + } else { + // AF field wasn't populated in info, so we don't have frequency information + // for this Variant. + // TODO instead of straight throwing an exception, log a warning. If at the end of this + // step the number of AlleleFreqs retrieved is below a given threshold, then throw an + // exception. + throw new IllegalArgumentException("Variant " + c.element().getId() + " does not have " + + "allele frequency information stored in INFO field AF."); + } + } + } + + /** + * Filters out AlleleFreqs for which the reference or alternate allele + * frequencies are below a minimum specified at construction. + */ + static class FilterFreq implements SerializableFunction, Boolean> { + + private final double minFreq; + + public FilterFreq(double minFreq) { + this.minFreq = minFreq; + } + + @Override + public Boolean apply(KV input) { + double freq = input.getValue().getRefFreq(); + if (freq >= minFreq && (1.0 - freq) >= minFreq) { + return true; + } + return false; + } + } + + /** + * Piles up reads and joins them against reference population statistics. + */ + static class PileupAndJoinReads + extends DoFn, KV> { + + private final TupleTag readCountsTag; + private final TupleTag refFreqTag; + + public PileupAndJoinReads(TupleTag readCountsTag, + TupleTag refFreqTag) { + this.readCountsTag = readCountsTag; + this.refFreqTag = refFreqTag; + } + + @Override + public void processElement(ProcessContext c) throws Exception { + AlleleFreq af = null; + af = c.element().getValue().getOnly(refFreqTag, null); + if (af == null) { + // no ref stats + return; + } + if (af.getAltBases().size() != 1) { + throw new IllegalArgumentException("Wrong number (" + af.getAltBases().size() + ") of" + + " alternate bases for Position " + c.element().getKey()); + } + + Iterable reads = c.element().getValue().getAll(readCountsTag); + + ImmutableMultiset.Builder rqSetBuilder = ImmutableMultiset.builder(); + for (ReadBaseQuality r : reads) { + ReadQualityCount.Base b; + if (af.getRefBases().equals(r.getBase())) { + b = ReadQualityCount.Base.REF; + } else if (af.getAltBases().get(0).equals(r.getBase())) { + b = ReadQualityCount.Base.NONREF; + } else { + b = ReadQualityCount.Base.OTHER; + } + ReadQualityCount rqc = new ReadQualityCount(); + rqc.setBase(b); + rqc.setQuality(r.getQuality()); + rqSetBuilder.add(rqc); + } + + ReadCounts rc = new ReadCounts(); + rc.setRefFreq(af.getRefFreq()); + for (Multiset.Entry entry : rqSetBuilder.build().entrySet()) { + ReadQualityCount rq = entry.getElement(); + rq.setCount(entry.getCount()); + rc.addReadQualityCount(rq); + } + c.output(KV.of(c.element().getKey(), rc)); + } + } + + /** + * Calls the Solver to maximize via a univariate function the results of the pipeline, inputted + * as a PCollectionView (the best way to retrieve our results as a Map in Dataflow). + */ + static class Maximizer extends DoFn { + + private final PCollectionView> view; + // Target absolute error for Brent's algorithm + private static final double ABS_ERR = 0.00001; + // Target relative error for Brent's algorithm + private static final double REL_ERR = 0.0001; + // Maximum number of evaluations of the Likelihood function in Brent's algorithm + private static final int MAX_EVAL = 100; + // Maximum number of iterations of Brent's algorithm + private static final int MAX_ITER = 100; + // Grid search step size + private static final double GRID_STEP = 0.05; + + public Maximizer(PCollectionView> view) { + this.view = view; + } + + @Override + public void processElement(ProcessContext c) throws Exception { + c.output(Double.toString(Solver.maximize(new LikelihoodFn(c.sideInput(view)), + 0.0, 0.5, GRID_STEP, REL_ERR, ABS_ERR, MAX_ITER, MAX_EVAL))); + } + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/GenomicsApiReader.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/GenomicsApiReader.java new file mode 100644 index 0000000..8067cd3 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/GenomicsApiReader.java @@ -0,0 +1,65 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers; + +import java.util.logging.Logger; + +import com.google.api.client.json.GenericJson; +import com.google.api.services.genomics.Genomics; +import com.google.cloud.dataflow.sdk.transforms.Aggregator; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.Sum; +import com.google.cloud.genomics.utils.GenomicsFactory; +import com.google.cloud.genomics.utils.OfflineAuth; + +public abstract class GenomicsApiReader + extends DoFn { + private static final Logger LOG = Logger.getLogger(GenomicsApiReader.class.getName()); + + // Used for access to the genomics API + protected final OfflineAuth auth; + protected final String fields; + protected Aggregator initializedRequestsCount; + protected Aggregator unsuccessfulResponsesCount; + protected Aggregator ioExceptionsCount; + protected Aggregator itemCount; + + public GenomicsApiReader(OfflineAuth auth, String fields) { + this.auth = auth; + this.fields = fields; + initializedRequestsCount = createAggregator("Genomics API Initialized Request Count", new Sum.SumIntegerFn()); + unsuccessfulResponsesCount = createAggregator("Genomics API Unsuccessful Response Count", new Sum.SumIntegerFn()); + ioExceptionsCount = createAggregator("Genomics API IOException Response Count", new Sum.SumIntegerFn()); + itemCount = createAggregator("Genomics API Item Count", new Sum.SumLongFn()); + } + + @Override + public void processElement(ProcessContext c) { + GenomicsFactory factory = GenomicsFactory.builder().build(); + Genomics genomics = factory.fromOfflineAuth(auth); + + processApiCall(genomics, c, c.element()); + + initializedRequestsCount.addValue(factory.initializedRequestsCount()); + unsuccessfulResponsesCount.addValue(factory.unsuccessfulResponsesCount()); + ioExceptionsCount.addValue(factory.ioExceptionsCount()); + LOG.info("ApiReader processed " + factory.initializedRequestsCount() + " requests (" + + factory.unsuccessfulResponsesCount() + " server errors and " + + factory.ioExceptionsCount() + " IO exceptions)"); + } + + protected abstract void processApiCall(Genomics genomics, ProcessContext c, I element); +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadGroupStreamer.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadGroupStreamer.java new file mode 100644 index 0000000..846f43b --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadGroupStreamer.java @@ -0,0 +1,88 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers; + +import java.util.Collections; +import java.util.List; + +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.PTransform; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.genomics.dataflow.utils.ShardOptions; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.cloud.genomics.utils.ShardBoundary; +import com.google.cloud.genomics.utils.ShardUtils; +import com.google.cloud.genomics.utils.ShardUtils.SexChromosomeFilter; +import com.google.genomics.v1.Read; +import com.google.genomics.v1.StreamReadsRequest; + +/** + * PTransform from a potentially large number of ReadGroupSets to streaming reads via gRPC. + * + * The sharding occurs as a stage of the pipeline, unlike the ReadStreamer PTransform + * where the shards are passed in. This is useful when the number of shards may + * potentially be larger than Dataflow's pipeline creation request size limit. + */ +public class ReadGroupStreamer extends PTransform, PCollection> { + protected final OfflineAuth auth; + protected final ShardBoundary.Requirement shardBoundary; + protected final String fields; + protected final SexChromosomeFilter sexChromosomeFilter; + + /** + * Create a streamer that can appropriately shard a potentially large number of ReadGroupSets. + * + * @param auth The OfflineAuth to use for the request. + * @param shardBoundary The shard boundary semantics to enforce. + * @param fields Which fields to include in a partial response or null for all. + * @param sexChromosomeFilter An enum value indicating how sex chromosomes should be + * handled in the result. + */ + public ReadGroupStreamer(OfflineAuth auth, ShardBoundary.Requirement shardBoundary, + String fields, SexChromosomeFilter sexChromosomeFilter) { + this.auth = auth; + this.shardBoundary = shardBoundary; + this.fields = fields; + this.sexChromosomeFilter = sexChromosomeFilter; + } + + @Override + public PCollection apply(PCollection readGroupSetIds) { + return readGroupSetIds.apply(ParDo.of(new CreateReadRequests())) + .apply(new ReadStreamer(auth, ShardBoundary.Requirement.STRICT, null)); + } + + private class CreateReadRequests extends DoFn { + + @Override + public void processElement(DoFn.ProcessContext c) + throws Exception { + ShardOptions options = c.getPipelineOptions().as(ShardOptions.class); + String readGroupSetId = c.element(); + + List requests = null; + if (options.isAllReferences()) { + requests = ShardUtils.getReadRequests(readGroupSetId, sexChromosomeFilter, options.getBasesPerShard(), auth); + } else { + requests = + ShardUtils.getReadRequests(Collections.singletonList(readGroupSetId), options.getReferences(), options.getBasesPerShard()); + } + for(StreamReadsRequest request : requests) { + c.output(request); + } + } + } +} + diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadReader.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadReader.java new file mode 100644 index 0000000..ce5883c --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadReader.java @@ -0,0 +1,73 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ + +package com.google.cloud.genomics.dataflow.readers; + +import java.util.logging.Logger; + +import com.google.api.services.genomics.Genomics; +import com.google.api.services.genomics.model.Read; +import com.google.api.services.genomics.model.SearchReadsRequest; +import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.cloud.genomics.utils.Paginator; +import com.google.cloud.genomics.utils.ShardBoundary; + +/** + * ReadReader is a DoFn that takes SearchReadsRequests, submits them + * to the Genomics API, and gives you Reads in return. + * It will take care of paging for you. You can optionally specify + * which fields you'd like returned. + */ +public class ReadReader extends GenomicsApiReader { + private static final Logger LOG = Logger.getLogger(ReadReader.class.getName()); + private final ShardBoundary.Requirement shardBoundary; + + /** + * Create a ReadReader using a auth and fields parameter. All fields not specified under + * readFields will not be returned in the API response. + * + * @param auth Auth class containing credentials. + * @param readFields Fields to return in responses. + */ + public ReadReader(OfflineAuth auth, ShardBoundary.Requirement shardBoundary, String readFields) { + super(auth, readFields); + this.shardBoundary = shardBoundary; + } + + /** + * Create a ReadReader with no fields parameter, all information will be returned. + * @param auth Auth class containing credentials. + */ + public ReadReader(OfflineAuth auth, ShardBoundary.Requirement shardBoundary) { + this(auth, shardBoundary, null); + } + + @Override + protected void processApiCall(Genomics genomics, ProcessContext c, SearchReadsRequest request) { + LOG.info("Starting Reads read loop"); + + GenomicsOptions options = c.getPipelineOptions().as(GenomicsOptions.class); + if (options.getPageSize() > 0) { + request.setPageSize(options.getPageSize()); + } + + for (Read read : Paginator.Reads.create(genomics, shardBoundary).search(request, fields)) { + c.output(read); + itemCount.addValue(1L); + } + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadStreamer.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadStreamer.java new file mode 100644 index 0000000..3dcdeb8 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadStreamer.java @@ -0,0 +1,116 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers; + +import java.io.IOException; +import java.security.GeneralSecurityException; +import java.util.Iterator; +import java.util.List; +import java.util.concurrent.TimeUnit; + +import com.google.cloud.dataflow.sdk.transforms.Aggregator; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.Max; +import com.google.cloud.dataflow.sdk.transforms.PTransform; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.transforms.Sum; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.cloud.genomics.utils.ShardBoundary; +import com.google.cloud.genomics.utils.grpc.ReadStreamIterator; +import com.google.common.base.Stopwatch; +import com.google.genomics.v1.Read; +import com.google.genomics.v1.StreamReadsRequest; +import com.google.genomics.v1.StreamReadsResponse; + +/** + * PTransform for streaming reads via gRPC. + */ +public class ReadStreamer extends +PTransform, PCollection> { + + protected final OfflineAuth auth; + protected final ShardBoundary.Requirement shardBoundary; + protected final String fields; + + /** + * Create a streamer that can enforce shard boundary semantics. + * + * @param auth The OfflineAuth to use for the request. + * @param shardBoundary The shard boundary semantics to enforce. + * @param fields Which fields to include in a partial response or null for all. + */ + public ReadStreamer(OfflineAuth auth, ShardBoundary.Requirement shardBoundary, String fields) { + this.auth = auth; + this.shardBoundary = shardBoundary; + this.fields = fields; + } + + @Override + public PCollection apply(PCollection input) { + return input.apply(ParDo.of(new RetrieveReads())) + .apply(ParDo.of(new ConvergeReadsList())); + } + + + private class RetrieveReads extends DoFn> { + + protected Aggregator initializedShardCount; + protected Aggregator finishedShardCount; + protected Aggregator shardTimeMaxSec; + + public RetrieveReads() { + initializedShardCount = createAggregator("Initialized Shard Count", new Sum.SumIntegerFn()); + finishedShardCount = createAggregator("Finished Shard Count", new Sum.SumIntegerFn()); + shardTimeMaxSec = createAggregator("Maximum Shard Processing Time (sec)", new Max.MaxLongFn()); + } + + @Override + public void processElement(ProcessContext c) throws IOException, GeneralSecurityException { + initializedShardCount.addValue(1); + shardTimeMaxSec.addValue(0L); + Stopwatch stopWatch = Stopwatch.createStarted(); + Iterator iter = ReadStreamIterator.enforceShardBoundary(auth, c.element(), shardBoundary, fields); + while (iter.hasNext()) { + StreamReadsResponse readResponse = iter.next(); + c.output(readResponse.getAlignmentsList()); + } + stopWatch.stop(); + shardTimeMaxSec.addValue(stopWatch.elapsed(TimeUnit.SECONDS)); + finishedShardCount.addValue(1); + } + } + + /** + * This step exists to emit the individual reads in a parallel step to the StreamReads step in + * order to increase throughput. + */ + private class ConvergeReadsList extends DoFn, Read> { + + protected Aggregator itemCount; + + public ConvergeReadsList() { + itemCount = createAggregator("Number of reads", new Sum.SumLongFn()); + } + + @Override + public void processElement(ProcessContext c) { + for (Read r : c.element()) { + c.output(r); + itemCount.addValue(1L); + } + } + } +} + diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/VariantReader.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/VariantReader.java new file mode 100644 index 0000000..7c09f45 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/VariantReader.java @@ -0,0 +1,71 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers; + +import java.util.logging.Logger; + +import com.google.api.services.genomics.Genomics; +import com.google.api.services.genomics.model.SearchVariantsRequest; +import com.google.api.services.genomics.model.Variant; +import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.cloud.genomics.utils.Paginator; +import com.google.cloud.genomics.utils.ShardBoundary; + +public class VariantReader extends GenomicsApiReader { + private static final Logger LOG = Logger.getLogger(VariantReader.class.getName()); + private final ShardBoundary.Requirement shardBoundary; + + /** + * Create a VariantReader using a auth and fields parameter. All fields not specified under + * variantFields will not be returned in the API response. + * + * @param auth Auth class containing credentials. + * @param variantFields Fields to return in responses. + */ + public VariantReader(OfflineAuth auth, ShardBoundary.Requirement shardBoundary, String variantFields) { + super(auth, variantFields); + this.shardBoundary = shardBoundary; + } + + /** + * Create a VariantReader with no fields parameter, all information will be returned. + * @param auth Auth class containing credentials. + */ + public VariantReader(OfflineAuth auth, ShardBoundary.Requirement shardBoundary) { + this(auth, shardBoundary, null); + } + + @Override + protected void processApiCall(Genomics genomics, ProcessContext c, final SearchVariantsRequest request) { + SearchVariantsRequest updatedRequest = request.clone(); + GenomicsOptions options = c.getPipelineOptions().as(GenomicsOptions.class); + if (options.getPageSize() > 0) { + updatedRequest.setPageSize(options.getPageSize()); + } + + LOG.info("Starting Variants read loop: " + updatedRequest); + int numberOfVariants = 0; + for (Variant variant : Paginator.Variants.create(genomics, shardBoundary).search(updatedRequest, fields)) { + c.output(variant); + ++numberOfVariants; + itemCount.addValue(1L); + } + + LOG.info("Read " + numberOfVariants + " variants at: " + updatedRequest.getReferenceName() + "-" + "[" + + updatedRequest.getStart() + ", " + updatedRequest.getEnd() + "]"); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/VariantStreamer.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/VariantStreamer.java new file mode 100644 index 0000000..8b88f32 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/VariantStreamer.java @@ -0,0 +1,124 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers; + +import java.io.IOException; +import java.security.GeneralSecurityException; +import java.util.Iterator; +import java.util.List; +import java.util.concurrent.TimeUnit; + +import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.cloud.dataflow.sdk.transforms.Aggregator; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.Max; +import com.google.cloud.dataflow.sdk.transforms.PTransform; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.transforms.Sum; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.cloud.genomics.utils.ShardBoundary; +import com.google.cloud.genomics.utils.grpc.VariantStreamIterator; +import com.google.common.base.Stopwatch; +import com.google.genomics.v1.StreamVariantsRequest; +import com.google.genomics.v1.StreamVariantsResponse; +import com.google.genomics.v1.Variant; + +/** + * PTransform for streaming variants via gRPC. + */ +public class VariantStreamer extends +PTransform, PCollection> { + + private static final Logger LOG = LoggerFactory.getLogger(VariantStreamer.class); + protected final OfflineAuth auth; + protected final ShardBoundary.Requirement shardBoundary; + protected final String fields; + + /** + * Create a streamer that can enforce shard boundary semantics. + * + * @param auth The OfflineAuth to use for the request. + * @param shardBoundary The shard boundary semantics to enforce. + * @param fields Which fields to include in a partial response or null for all. + */ + public VariantStreamer(OfflineAuth auth, ShardBoundary.Requirement shardBoundary, String fields) { + this.auth = auth; + this.shardBoundary = shardBoundary; + this.fields = fields; + } + + @Override + public PCollection apply(PCollection input) { + return input.apply(ParDo.of(new RetrieveVariants())) + .apply(ParDo.of(new ConvergeVariantsList())); + } + + private class RetrieveVariants extends DoFn> { + + protected Aggregator initializedShardCount; + protected Aggregator finishedShardCount; + protected Aggregator shardTimeMaxSec; + DescriptiveStatistics stats; + + public RetrieveVariants() { + initializedShardCount = createAggregator("Initialized Shard Count", new Sum.SumIntegerFn()); + finishedShardCount = createAggregator("Finished Shard Count", new Sum.SumIntegerFn()); + shardTimeMaxSec = createAggregator("Maximum Shard Processing Time (sec)", new Max.MaxLongFn()); + stats = new DescriptiveStatistics(500); + } + + @Override + public void processElement(ProcessContext c) throws IOException, GeneralSecurityException, InterruptedException { + initializedShardCount.addValue(1); + shardTimeMaxSec.addValue(0L); + Stopwatch stopWatch = Stopwatch.createStarted(); + Iterator iter = VariantStreamIterator.enforceShardBoundary(auth, c.element(), shardBoundary, fields); + while (iter.hasNext()) { + StreamVariantsResponse variantResponse = iter.next(); + c.output(variantResponse.getVariantsList()); + } + stopWatch.stop(); + shardTimeMaxSec.addValue(stopWatch.elapsed(TimeUnit.SECONDS)); + stats.addValue(stopWatch.elapsed(TimeUnit.SECONDS)); + finishedShardCount.addValue(1); + LOG.info("Shard Duration in Seconds - Min: " + stats.getMin() + " Max: " + stats.getMax() + + " Avg: " + stats.getMean() + " StdDev: " + stats.getStandardDeviation()); + } + } + + /** + * This step exists to emit the individual variants in a parallel step to the StreamVariants step + * in order to increase throughput. + */ + private class ConvergeVariantsList extends DoFn, Variant> { + + protected Aggregator itemCount; + + public ConvergeVariantsList() { + itemCount = createAggregator("Number of variants", new Sum.SumLongFn()); + } + + @Override + public void processElement(ProcessContext c) { + for (Variant v : c.element()) { + c.output(v); + itemCount.addValue(1L); + } + } + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/BAMIO.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/BAMIO.java new file mode 100644 index 0000000..cebd15b --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/BAMIO.java @@ -0,0 +1,93 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers.bam; + +import com.google.api.services.storage.Storage; + +import htsjdk.samtools.SamInputResource; +import htsjdk.samtools.SamReader; +import htsjdk.samtools.SamReaderFactory; +import htsjdk.samtools.ValidationStringency; +import htsjdk.samtools.seekablestream.SeekableStream; + +import java.io.IOException; +import java.util.logging.Logger; + +/** + * Utility methods for opening BAM files from GCS storage using HTSJDK. + * For sharding in pipelines we need access to the guts of BAM index, + * so openBAMAndExposeIndex provides a convenient way to get both SamReader and + * a stream for an index file. + */ +public class BAMIO { + public static class ReaderAndIndex { + public SamReader reader; + public SeekableStream index; + } + private static final Logger LOG = Logger.getLogger(BAMIO.class.getName()); + + public static ReaderAndIndex openBAMAndExposeIndex(Storage.Objects storageClient, String gcsStoragePath, ValidationStringency stringency) throws IOException { + ReaderAndIndex result = new ReaderAndIndex(); + result.index = openIndexForPath(storageClient, gcsStoragePath); + result.reader = openBAMReader( + openBAMFile(storageClient, gcsStoragePath,result.index), stringency, false); + return result; + } + + public static SamReader openBAM(Storage.Objects storageClient, String gcsStoragePath, + ValidationStringency stringency, boolean includeFileSource) throws IOException { + return openBAMReader(openBAMFile(storageClient, gcsStoragePath, + openIndexForPath(storageClient, gcsStoragePath)), stringency, includeFileSource); + } + + public static SamReader openBAM(Storage.Objects storageClient, String gcsStoragePath, ValidationStringency stringency) throws IOException { + return openBAM(storageClient, gcsStoragePath, stringency, false); + } + + private static SeekableStream openIndexForPath(Storage.Objects storageClient,String gcsStoragePath) { + final String indexPath = gcsStoragePath + ".bai"; + try { + return new SeekableGCSStream(storageClient, indexPath); + } catch (IOException ex) { + LOG.info("No index for " + indexPath); + // Ignore if there is no bai file + } + return null; + } + + private static SamInputResource openBAMFile(Storage.Objects storageClient, String gcsStoragePath, SeekableStream index) throws IOException { + SamInputResource samInputResource = + SamInputResource.of(new SeekableGCSStream(storageClient, gcsStoragePath)); + if (index != null) { + samInputResource.index(index); + } + + LOG.info("getReadsFromBAMFile - got input resources"); + return samInputResource; + } + + private static SamReader openBAMReader(SamInputResource resource, ValidationStringency stringency, boolean includeFileSource) { + SamReaderFactory samReaderFactory = SamReaderFactory + .makeDefault() + .validationStringency(stringency) + .enable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES); + if (includeFileSource) { + samReaderFactory.enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS); + } + final SamReader samReader = samReaderFactory.open(resource); + return samReader; + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/BAMShard.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/BAMShard.java new file mode 100644 index 0000000..c7250e5 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/BAMShard.java @@ -0,0 +1,117 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers.bam; + +import com.google.cloud.genomics.utils.Contig; +import com.google.common.collect.Lists; + +import htsjdk.samtools.BAMFileIndexImpl; +import htsjdk.samtools.Chunk; +import htsjdk.samtools.SAMFileSpanImpl; + +import java.io.Serializable; +import java.util.List; + +/** + * A shard of BAM data we will create during sharding and then use to drive the reading. + * We use this class during shard generation, by iteratively building + * a shard, extending it bin by bin (@see #addBin) + * At the end of the process, the shard is finalized (@see #finalize) + * and SAMFileSpan that has all the chunks we want to read is produced. + */ +public class BAMShard implements Serializable { + public String file; + public SAMFileSpanImpl span; + public Contig contig; + public List chunks; + public long cachedSizeInBytes = -1; + + /** + * Begins a new shard with an empty chunk list and a starting locus. + */ + public BAMShard(String file, String referenceName, long firstLocus) { + this.file = file; + this.contig = new Contig(referenceName, firstLocus, -1); + this.chunks = Lists.newLinkedList(); + this.span = null; + } + + /** + * Creates a shard with a known file span. + * Such shard is not expected to be extended and calling addBin or finalize on it will fail. + * This constructor is used for "degenerate" shards like unmapped reads or + * all reads in cases where we don't have an index. + */ + public BAMShard(String file, SAMFileSpanImpl span, Contig contig) { + this.file = file; + this.span = span; + this.contig = contig; + this.chunks = null; + } + + /** + * Appends chunks from another bin to the list and moved the end position. + */ + public void addBin(List chunksToAdd, long lastLocus) { + assert chunks != null; + contig = new Contig(contig.referenceName, contig.start, lastLocus); + chunks.addAll(chunksToAdd); + updateSpan(); + } + + /** + * Generates a final list of chunks, now that we know the exact bounding loci + * for this shard. We get all chunks overlapping this loci, and then ask the index + * for the chunks overlapping them. + */ + public BAMShard finalize(BAMFileIndexImpl index, long lastLocus) { + contig = new Contig(contig.referenceName, contig.start, lastLocus); + this.chunks = index.getChunksOverlapping(contig.referenceName, + (int)contig.start, (int)contig.end); + updateSpan(); + return this; + } + + /** + * Updates the underlying file span by optimizing and coalescing the current chunk list. + */ + private void updateSpan() { + span = new SAMFileSpanImpl(Chunk.optimizeChunkList(chunks, this.contig.start)); + cachedSizeInBytes = -1; + } + + public long sizeInLoci() { + return contig.end > 0 ? contig.end - contig.start : 0; + } + + public long approximateSizeInBytes() { + if (cachedSizeInBytes < 0) { + cachedSizeInBytes = span.approximateSizeInBytes(); + } + return cachedSizeInBytes; + } + + @Override + public String toString() { + String str = file + ": " + contig.toString() + ", locus size = " + sizeInLoci(); + if (cachedSizeInBytes >= 0) { + // Only return this as part of the string if it's already cached and calculated. + // Otherwise calling this function causes the object to be mutated. + str += ", span size = " + cachedSizeInBytes; + } + return str; + } +} \ No newline at end of file diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/ReadBAMTransform.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/ReadBAMTransform.java new file mode 100644 index 0000000..05156c4 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/ReadBAMTransform.java @@ -0,0 +1,139 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers.bam; + +import com.google.api.services.genomics.model.Read; +import com.google.api.services.storage.Storage; +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.coders.SerializableCoder; +import com.google.cloud.dataflow.sdk.coders.StringUtf8Coder; +import com.google.cloud.dataflow.sdk.transforms.Aggregator; +import com.google.cloud.dataflow.sdk.transforms.Create; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.PTransform; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.transforms.View; +import com.google.cloud.dataflow.sdk.transforms.Sum.SumIntegerFn; +import com.google.cloud.dataflow.sdk.util.Transport; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.dataflow.sdk.values.PCollectionTuple; +import com.google.cloud.dataflow.sdk.values.PCollectionView; +import com.google.cloud.dataflow.sdk.values.TupleTag; +import com.google.cloud.genomics.dataflow.utils.GCSOptions; +import com.google.cloud.genomics.utils.Contig; +import com.google.cloud.genomics.utils.OfflineAuth; + +import htsjdk.samtools.ValidationStringency; + +import java.io.IOException; +import java.util.Arrays; +import java.util.List; + +/** + * Takes a tuple of 2 collections: Contigs and BAM files and transforms them into + * a collection of reads by reading BAM files in a sharded manner. + */ +public class ReadBAMTransform extends PTransform, PCollection> { + OfflineAuth auth; + ReaderOptions options; + + public static class ReadFn extends DoFn { + OfflineAuth auth; + Storage.Objects storage; + ReaderOptions options; + Aggregator recordCountAggregator; + Aggregator readCountAggregator; + Aggregator skippedStartCountAggregator; + Aggregator skippedEndCountAggregator; + Aggregator skippedRefMismatchAggregator; + + public ReadFn(OfflineAuth auth, ReaderOptions options) { + this.auth = auth; + this.options = options; + recordCountAggregator = createAggregator("Processed records", new SumIntegerFn()); + readCountAggregator = createAggregator("Reads generated", new SumIntegerFn()); + skippedStartCountAggregator = createAggregator("Skipped start", new SumIntegerFn()); + skippedEndCountAggregator = createAggregator("Skipped end", new SumIntegerFn()); + skippedRefMismatchAggregator = createAggregator("Ref mismatch", new SumIntegerFn()); + } + + @Override + public void startBundle(DoFn.Context c) throws IOException { + storage = Transport.newStorageClient(c.getPipelineOptions().as(GCSOptions.class)).build().objects(); + } + + @Override + public void processElement(ProcessContext c) throws java.lang.Exception { + final Reader reader = new Reader(storage, options, c.element(), c); + reader.process(); + recordCountAggregator.addValue(reader.recordsProcessed); + skippedStartCountAggregator.addValue(reader.recordsBeforeStart); + skippedEndCountAggregator.addValue(reader.recordsAfterEnd); + skippedRefMismatchAggregator.addValue(reader.mismatchedSequence); + readCountAggregator.addValue(reader.readsGenerated); + } + } + + // ---------------------------------------------------------------- + // back to ReadBAMTransform + + public static PCollection getReadsFromBAMFilesSharded( + Pipeline p, + OfflineAuth auth, + Iterable contigs, + ReaderOptions options, + String BAMFile, + ShardingPolicy shardingPolicy) throws IOException { + ReadBAMTransform readBAMSTransform = new ReadBAMTransform(options); + readBAMSTransform.setAuth(auth); + + final Storage.Objects storage = Transport + .newStorageClient(p.getOptions().as(GCSOptions.class)).build().objects(); + + + final List shardsList = Sharder.shardBAMFile(storage, BAMFile, contigs, + shardingPolicy); + + PCollection shards = p.apply(Create + .of(shardsList)) + .setCoder(SerializableCoder.of(BAMShard.class)); + + return readBAMSTransform.apply(shards); + } + + @Override + public PCollection apply(PCollection shards) { + final PCollection reads = shards.apply(ParDo + .of(new ReadFn(auth, options))); + + return reads; + } + + public OfflineAuth getAuth() { + return auth; + } + + public void setAuth(OfflineAuth auth) { + this.auth = auth; + } + + // non-public methods + + protected ReadBAMTransform(ReaderOptions options) { + super(); + this.options = options; + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/Reader.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/Reader.java new file mode 100644 index 0000000..9130a21 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/Reader.java @@ -0,0 +1,242 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers.bam; + +import com.google.api.services.genomics.model.Read; +import com.google.api.services.storage.Storage; +import com.google.api.services.storage.Storage.Objects; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.genomics.utils.Contig; +import com.google.cloud.genomics.utils.ReadUtils; +import com.google.common.base.Stopwatch; + +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMRecordIterator; +import htsjdk.samtools.SamReader; +import htsjdk.samtools.ValidationStringency; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.List; +import java.util.concurrent.TimeUnit; +import java.util.logging.Logger; + +/** + * Get all the reads specified by a given shard from a given BAM file. + * Meant to be called from the DoFn processing the shard. + */ +public class Reader { + private static final Logger LOG = Logger.getLogger(Reader.class.getName()); + + Storage.Objects storageClient; + BAMShard shard; + DoFn.ProcessContext c; + Stopwatch timer; + ReaderOptions options; + + SAMRecordIterator iterator; + enum Filter { + UNMAPPED_ONLY, + MAPPED_AND_UNMAPPED, + MAPPED_ONLY + } + + Filter filter; + + public int recordsBeforeStart = 0; + public int recordsAfterEnd = 0; + public int mismatchedSequence = 0; + public int recordsProcessed = 0; + public int readsGenerated = 0; + + public Reader(Objects storageClient, ReaderOptions options, BAMShard shard, DoFn.ProcessContext c) { + super(); + this.storageClient = storageClient; + this.shard = shard; + this.c = c; + this.options = options; + filter = setupFilter(options, shard.contig.referenceName); + } + + public static Filter setupFilter(ReaderOptions options, String referenceName) { + /* + * The common way of asking for unmapped reads is by specifying asterisk + * as the sequence name. + * From SAM format, section 1.4. paragraph 3: + * "RNAME: Reference sequence NAME of the alignment. + * If @SQ header lines are present, RNAME (if not ‘*’) must be present in + * one of the SQ-SN tag. + * An unmapped segment without coordinate has a ‘*’ at this field." + * https://samtools.github.io/hts-specs/SAMv1.pdf + */ + if (referenceName.equals("*")) { + return Filter.UNMAPPED_ONLY; + } else if (options.getIncludeUnmappedReads()) { + return Filter.MAPPED_AND_UNMAPPED; + } + return Filter.MAPPED_ONLY; + } + + public void process() throws IOException { + timer = Stopwatch.createStarted(); + openFile(); + + while (iterator.hasNext()) { + processRecord(iterator.next()); + } + + dumpStats(); + } + + void openFile() throws IOException { + LOG.info("Processing shard " + shard); + final SamReader reader = BAMIO.openBAM(storageClient, shard.file, + options.getStringency()); + iterator = null; + if (reader.hasIndex() && reader.indexing() != null) { + if (filter == Filter.UNMAPPED_ONLY) { + LOG.info("Processing unmapped"); + iterator = reader.queryUnmapped(); + } else if (shard.span != null) { + LOG.info("Processing span for " + shard.contig); + iterator = reader.indexing().iterator(shard.span); + } else if (shard.contig.referenceName != null && !shard.contig.referenceName.isEmpty()) { + LOG.info("Processing all bases for " + shard.contig); + iterator = reader.query(shard.contig.referenceName, (int) shard.contig.start, + (int) shard.contig.end, false); + } + } + if (iterator == null) { + LOG.info("Processing all reads"); + iterator = reader.iterator(); + } + } + + /** + * Checks if the record matches our filter. + */ + static boolean passesFilter(SAMRecord record, Filter filter, + String referenceName) { + // If we are looking for only mapped or only unmapped reads then we will use + // the UnmappedFlag to decide if this read should be rejected. + if (filter == Filter.UNMAPPED_ONLY && !record.getReadUnmappedFlag()) { + return false; + } + + if (filter == Filter.MAPPED_ONLY && record.getReadUnmappedFlag()) { + return false; + } + + // If we are looking for mapped reads, then we check the reference name + // of the read matches the one we are looking for. + final boolean referenceNameMismatch = referenceName != null && + !referenceName.isEmpty() && + !referenceName.equals(record.getReferenceName()); + + // Note that unmapped mate pair of mapped read will have a reference + // name set to the reference of its mapped mate. + if ((filter == Filter.MAPPED_ONLY || filter == Filter.MAPPED_AND_UNMAPPED) + && referenceNameMismatch) { + return false; + } + + return true; + } + + boolean passesFilter(SAMRecord record) { + return passesFilter(record, filter, shard.contig.referenceName); + } + + void processRecord(SAMRecord record) { + recordsProcessed++; + if (!passesFilter(record)) { + mismatchedSequence++; + return; + } + if (record.getAlignmentStart() < shard.contig.start) { + recordsBeforeStart++; + return; + } + if (record.getAlignmentStart() > shard.contig.end) { + recordsAfterEnd++; + return; + } + c.output(ReadUtils.makeRead(record)); + readsGenerated++; + } + + void dumpStats() { + timer.stop(); + long elapsed = timer.elapsed(TimeUnit.MILLISECONDS); + if (elapsed == 0) elapsed = 1; + LOG.info("Processed " + recordsProcessed + " outputted " + readsGenerated + + " in " + timer + + ". Speed: " + (recordsProcessed*1000)/elapsed + " reads/sec" + + ", filtered out by reference and mapping " + mismatchedSequence + + ", skippedBefore " + recordsBeforeStart + + ", skipped after " + recordsAfterEnd); + } + + /** + * To compare how sharded reading works vs. plain HTSJDK sequential iteration, + * this method implements such iteration. + * This makes it easier to discover errors such as reads that are somehow + * skipped by a sharded approach. + */ + public static Iterable readSequentiallyForTesting(Objects storageClient, + String storagePath, Contig contig, + ReaderOptions options) throws IOException { + Stopwatch timer = Stopwatch.createStarted(); + SamReader samReader = BAMIO.openBAM(storageClient, storagePath, options.getStringency()); + SAMRecordIterator iterator = samReader.queryOverlapping(contig.referenceName, + (int) contig.start + 1, + (int) contig.end); + List reads = new ArrayList(); + + int recordsBeforeStart = 0; + int recordsAfterEnd = 0; + int mismatchedSequence = 0; + int recordsProcessed = 0; + Filter filter = setupFilter(options, contig.referenceName); + while (iterator.hasNext()) { + SAMRecord record = iterator.next(); + final boolean passesFilter = passesFilter(record, filter, contig.referenceName); + + if (!passesFilter) { + mismatchedSequence++; + continue; + } + if (record.getAlignmentStart() < contig.start) { + recordsBeforeStart++; + continue; + } + if (record.getAlignmentStart() > contig.end) { + recordsAfterEnd++; + continue; + } + reads.add(ReadUtils.makeRead(record)); + recordsProcessed++; + } + timer.stop(); + LOG.info("NON SHARDED: Processed " + recordsProcessed + + " in " + timer + + ". Speed: " + (recordsProcessed*1000)/timer.elapsed(TimeUnit.MILLISECONDS) + " reads/sec" + + ", skipped other sequences " + mismatchedSequence + + ", skippedBefore " + recordsBeforeStart + + ", skipped after " + recordsAfterEnd); + return reads; + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/ReaderOptions.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/ReaderOptions.java new file mode 100644 index 0000000..5b9c34b --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/ReaderOptions.java @@ -0,0 +1,63 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers.bam; + +import htsjdk.samtools.ValidationStringency; + +import java.io.Serializable; + +/** + * A collection of options governing how BAM files are read. + */ +public class ReaderOptions implements Serializable{ + ValidationStringency stringency = ValidationStringency.DEFAULT_STRINGENCY; + + /** + * If true, we will read and return unmapped reads in the order expected by + * HTSDK/GATK/Picard tools, specifically unmapped mate pairs of mapped reads + * will be returned according to their position specified in the BAM record + * (as opposed to being after all the mapped reads). This position is + * typically specified such that these unmapped mates immediately follow + * their mapped counterparts. + */ + boolean includeUnmappedReads = false; + + public ReaderOptions() { + + } + + public ReaderOptions(ValidationStringency stringency, boolean includeUnmappedReads) { + this.stringency = stringency; + this.includeUnmappedReads = includeUnmappedReads; + } + + public ValidationStringency getStringency() { + return stringency; + } + + public void setStringency(ValidationStringency stringency) { + this.stringency = stringency; + } + + public boolean getIncludeUnmappedReads() { + return includeUnmappedReads; + } + + public void setIncludeUnmappedReads(boolean includeUnmappedReads) { + this.includeUnmappedReads = includeUnmappedReads; + } +} + diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/SeekableGCSStream.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/SeekableGCSStream.java new file mode 100644 index 0000000..b879bee --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/SeekableGCSStream.java @@ -0,0 +1,243 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers.bam; + +import com.google.api.client.http.HttpResponse; +import com.google.api.services.storage.Storage; +import com.google.api.services.storage.Storage.Objects.Get; +import com.google.api.services.storage.model.StorageObject; + +import htsjdk.samtools.seekablestream.SeekableStream; + +import java.io.IOException; +import java.io.InputStream; +import java.util.logging.Level; +import java.util.logging.Logger; +import java.util.regex.Pattern; + +/** + * Adapter of GCS to look like HTSJDK SeekableStream so BAM readers + * can stream data from GCS. + * TODO: implement more sophisticated retries with backoff. + */ +public class SeekableGCSStream extends SeekableStream { + private static final Logger LOG = Logger.getLogger(SeekableGCSStream.class.getName()); + + private static final Pattern SLASH = Pattern.compile("/"); + private static final String GCS_PREFIX = "gs://"; + private static final int MAX_RETRIES = 3; + private static final long RETRY_SLEEP_TIME_MSEC = 1000; + + private Storage.Objects client; + private StorageObject object; + private String name; + private Get get; + private InputStream stream = null; + private long size = -1; + private long position = -1; + private byte[] oneByte = new byte[1]; + private boolean atEof = false; + + public SeekableGCSStream(Storage.Objects client, String name) throws IOException { + LOG.info("Creating SeekableGCSStream: " + name); + this.client = client; + object = uriToStorageObject(name); + get = this.client.get(object.getBucket(), object.getName()); + seek(0); + } + + @Override + public void close() throws IOException { + if (stream != null) { + stream.close(); + stream = null; + } + } + + @Override + public boolean eof() throws IOException { + return atEof; + } + + @Override + public String getSource() { + return name; + } + + @Override + public long length() { + return size; + } + + @Override + public long position() throws IOException { + return position; + } + + @Override + public int read() throws IOException { + final int bytesRead = read(oneByte, 0, 1); + return bytesRead==1 ? oneByte[0] : -1; + } + + @Override + public void seek(long arg0) throws IOException { + if (arg0 == position) { + return; + } + validatePosition(arg0); + position = arg0; + openStream(); + } + + protected void openStream() + throws IOException { + if (LOG.isLoggable(Level.FINEST)) { + LOG.finest("openStream: " + position); + } + try { + close(); + } catch (Exception ex) { + // Ignore problems in closing the old stream + } + validatePosition(position); + get.getRequestHeaders() + .setRange(String.format("bytes=%d-", position)); + HttpResponse response; + try { + response = get.executeMedia(); + } catch (IOException e) { + String msg = String.format("Error reading %s at position %d", + name, position); + atEof = true; + throw new IOException(msg, e); + } + String contentRange = response.getHeaders().getContentRange(); + if (response.getHeaders().getContentLength() != null) { + size = response.getHeaders().getContentLength() + position; + } else if (contentRange != null) { + String sizeStr = SLASH.split(contentRange)[1]; + try { + size = Long.parseLong(sizeStr); + } catch (NumberFormatException e) { + throw new IOException( + "Could not determine size from response from Content-Range: " + contentRange, e); + } + } else { + throw new IOException("Could not determine size of response"); + } + if (LOG.isLoggable(Level.FINEST)) { + LOG.finest("stream size=" + size); + } + atEof = size == 0; + stream = response.getContent(); + } + + protected void validatePosition(long newPosition) { + if (newPosition < 0) { + throw new IllegalArgumentException( + String.format("Invalid seek offset: position value (%d) must be >= 0", newPosition)); + } + + if ((size >= 0) && (newPosition >= size)) { + throw new IllegalArgumentException( + String.format( + "Invalid seek offset: position value (%d) must be between 0 and %d", + newPosition, size)); + } + } + + @Override + public int read(byte[] buf, int offset, int len) + throws IOException { + if (LOG.isLoggable(Level.FINEST)) { + LOG.finest("Read at offset " + offset + " length " + len); + } + if (len == 0 || offset >= len) { + return 0; + } + + int totalBytesRead = 0; + int retriesAttempted = 0; + + do { + try { + final int numBytesRead = stream.read(buf, + offset + totalBytesRead, len - totalBytesRead); + if (LOG.isLoggable(Level.FINEST)) { + LOG.finest("Read returned: " + numBytesRead); + } + if (numBytesRead < 0) { + atEof = true; + break; + } + totalBytesRead += numBytesRead; + position += numBytesRead; + + retriesAttempted = 0; + } catch (IOException ioe) { + if (retriesAttempted == MAX_RETRIES) { + LOG.warning( + String.format("Already attempted max of %d retries while reading '%s'; throwing exception.", + retriesAttempted, name)); + throw ioe; + } else { + ++retriesAttempted; + LOG.warning(String.format("Got exception: %s while reading '%s'; retry # %d. Sleeping...", + ioe.getMessage(), name, retriesAttempted)); + + try { + // TODO: implement backoff logic instead of simplistic static sleep interval + Thread.sleep(RETRY_SLEEP_TIME_MSEC); + } catch (InterruptedException ie) { + LOG.warning(String.format("Interrupted while sleeping before retry. Giving up " + + "after %d retries for '%s'", retriesAttempted, name)); + ioe.addSuppressed(ie); + throw ioe; + } + LOG.info(String.format("Done sleeping before retry for '%s'; retry # %d.", + name, retriesAttempted)); + + openStream(); + } + } + } while (totalBytesRead < len); + + final int retVal = (totalBytesRead == 0) ? -1 : totalBytesRead; + if (LOG.isLoggable(Level.FINEST)) { + LOG.finest("Read result " + retVal); + } + return retVal; + } + + private static StorageObject uriToStorageObject(String uri) throws IOException { + StorageObject object = new StorageObject(); + if (uri.startsWith(GCS_PREFIX)) { + uri = uri.substring(GCS_PREFIX.length()); + } else { + throw new IOException("Invalid GCS path (does not start with gs://): " + uri); + } + int slashPos = uri.indexOf("/"); + if (slashPos > 0) { + object.setBucket(uri.substring(0, slashPos)); + object.setName(uri.substring(slashPos + 1)); + LOG.info("uriToStorageObject " + uri + "=" + object.getBucket() + ":" + object.getName()); + } else { + throw new IOException("Invalid GCS path (does not have bucket/name form): " + uri); + } + return object; + } +} \ No newline at end of file diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/Sharder.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/Sharder.java new file mode 100644 index 0000000..ec2dcf1 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/Sharder.java @@ -0,0 +1,252 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers.bam; + +import com.google.api.services.storage.Storage; +import com.google.api.services.storage.Storage.Objects; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.genomics.utils.Contig; +import com.google.common.base.Function; +import com.google.common.collect.Iterables; +import com.google.common.collect.Lists; +import com.google.common.collect.Maps; + +import htsjdk.samtools.BAMFileIndexImpl; +import htsjdk.samtools.Bin; +import htsjdk.samtools.Chunk; +import htsjdk.samtools.GenomicIndexUtil; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMSequenceRecord; +import htsjdk.samtools.SamReader; +import htsjdk.samtools.ValidationStringency; +import htsjdk.samtools.seekablestream.SeekableStream; +import htsjdk.samtools.util.IOUtil; + +import java.io.IOException; +import java.util.BitSet; +import java.util.HashMap; +import java.util.List; +import java.util.logging.Level; +import java.util.logging.Logger; + +import javax.annotation.Nullable; + +/** + * Generates shards for a given BAM file and a desired set of contigs. + */ +public class Sharder { + private static final Logger LOG = Logger.getLogger(Sharder.class.getName()); + + public interface SharderOutput { + public void output(BAMShard shard); + } + + Storage.Objects storageClient; + String filePath; + Iterable requestedContigs; + SharderOutput output; + final ShardingPolicy shardingPolicy; + + SamReader reader; + SeekableStream indexStream; + SAMFileHeader header; + BAMFileIndexImpl index; + + boolean allReferences; + boolean hasIndex; + HashMap contigsByReference; + + public static List shardBAMFile(Objects storageClient, + String filePath, Iterable requestedContigs, + ShardingPolicy shardingPolicy) throws IOException { + final List shards = Lists.newArrayList(); + (new Sharder(storageClient, filePath, requestedContigs, shardingPolicy, + new SharderOutput() { + @Override + public void output(BAMShard shard) { + shards.add(shard); + } + })) + .process(); + return shards; + } + + public Sharder(Objects storageClient, String filePath, Iterable requestedContigs, + ShardingPolicy shardingPolicy, + SharderOutput output) { + super(); + this.storageClient = storageClient; + this.filePath = filePath; + this.shardingPolicy = shardingPolicy; + // HTSJDK expects 1-based coordinates - need to shift by 1 + this.requestedContigs = Iterables.transform(requestedContigs, + new Function() { + @Override + @Nullable + public Contig apply(@Nullable Contig arg0) { + return new Contig(arg0.referenceName, arg0.start + 1, arg0.end); + } + }); + this.output = output; + } + + public void process() throws IOException { + LOG.info("Processing BAM file " + filePath); + + openFile(); + processHeader(); + + for (SAMSequenceRecord sequenceRecord : header.getSequenceDictionary().getSequences()) { + final Contig contig = desiredContigForReference(sequenceRecord); + if (contig == null) { + continue; + } else if (!hasIndex) { + // No index, so create a shard over all BAM file and pass a contig restrict. + // We will iterate over all reads for this reference and skip the ones outside contig. + LOG.info("No index: outputting shard for " + contig); + output.output(new BAMShard(filePath, null, contig)); + continue; + } + createShardsForReference(sequenceRecord, contig); + } + if (index != null) { + index.close(); + } + } + + void openFile() throws IOException { + final BAMIO.ReaderAndIndex r = BAMIO.openBAMAndExposeIndex(storageClient, filePath, ValidationStringency.DEFAULT_STRINGENCY); + reader = r.reader; + indexStream = r.index; + header = reader.getFileHeader(); + hasIndex = reader.hasIndex() && reader.indexing().hasBrowseableIndex(); + LOG.info("Has index = " + hasIndex); + if (hasIndex) { + index = new BAMFileIndexImpl( + IOUtil.maybeBufferedSeekableStream(indexStream),header.getSequenceDictionary()); + } else { + index = null; + } + } + + void processHeader() { + contigsByReference = Maps.newHashMap(); + for (Contig contig : requestedContigs) { + contigsByReference.put(contig.referenceName != null ? contig.referenceName : "", contig); + } + if (contigsByReference.size() == 0 || contigsByReference.containsKey("*")) { + LOG.info("Outputting unmapped reads shard "); + output.output(new BAMShard(filePath, null, new Contig("*", 0, -1))); + } + allReferences = + contigsByReference.size() == 0 || contigsByReference.containsKey(""); + LOG.info("All references = " + allReferences); + LOG.info("BAM has index = " + reader.hasIndex()); + LOG.info("BAM has browseable index = " + reader.indexing().hasBrowseableIndex()); + LOG.info("Class for index = " + reader.indexing().getIndex().getClass().getName()); + } + + Contig desiredContigForReference(SAMSequenceRecord reference) { + Contig contig = contigsByReference.get(reference.getSequenceName()); + if (contig == null) { + if (allReferences) { + contig = new Contig(reference.getSequenceName(), 0, -1); + } else { + LOG.fine("No contig requested for reference " + reference.getSequenceName()); + return null; + } + } + assert contig != null; + if (contig.end <= 0) { + contig = new Contig(contig.referenceName, contig.start, reference.getSequenceLength()); + LOG.info("Updated length for contig for " + contig.referenceName + " to " + contig.end); + } + return contig; + } + + void createShardsForReference(SAMSequenceRecord reference, Contig contig) { + LOG.info("Creating shard for: " + contig); + final BitSet overlappingBins = GenomicIndexUtil.regionToBins( + (int) contig.start, (int) contig.end); + if (overlappingBins == null) { + LOG.warning("No overlapping bins for " + contig.start + ":" + contig.end); + return; + } + + + BAMShard currentShard = null; + for (int binIndex = overlappingBins.nextSetBit(0); binIndex >= 0; binIndex = overlappingBins.nextSetBit(binIndex + 1)) { + final Bin bin = index.getBinData(reference.getSequenceIndex(), binIndex); + if (bin == null) { + continue; + } + if (LOG.isLoggable(Level.FINE)) { + LOG.fine("Processing bin " + index.getFirstLocusInBin(bin) + "-" + + index.getLastLocusInBin(bin)); + } + + if (index.getLevelForBin(bin) != (GenomicIndexUtil.LEVEL_STARTS.length - 1)) { + if (LOG.isLoggable(Level.FINEST)) { + LOG.finest("Skipping - not lowest"); + } + continue; + // Skip non-lowest level bins + // Its ok to skip higher level bins + // because in BAMShard#finalize we + // will get all chunks overlapping a genomic region that + // we end up having for the shard, so we will not + // miss any reads on the boundary. + } + final List chunksInBin = bin.getChunkList(); + if (chunksInBin.isEmpty()) { + if (LOG.isLoggable(Level.FINEST)) { + LOG.finest("Skipping - empty"); + } + continue; // Skip empty bins + } + + if (currentShard == null) { + int startLocus = + Math.max(index.getFirstLocusInBin(bin), (int)contig.start); + + if (LOG.isLoggable(Level.FINE)) { + LOG.fine("Creating shard starting from " + startLocus); + } + currentShard = new BAMShard(filePath, reference.getSequenceName(), + startLocus); + } + currentShard.addBin(chunksInBin, index.getLastLocusInBin(bin)); + if (LOG.isLoggable(Level.FINE)) { + LOG.fine("Extending the shard to " + index.getLastLocusInBin(bin)); + } + + if (shardingPolicy.shardBigEnough(currentShard)) { + LOG.info("Shard size is big enough to finalize: " + + currentShard.sizeInLoci() + ", " + currentShard.approximateSizeInBytes() + " bytes"); + final BAMShard bamShard = currentShard.finalize(index, Math.min(index.getLastLocusInBin(bin), (int)contig.end)); + LOG.info("Outputting shard: " + bamShard.contig); + output.output(bamShard); + currentShard = null; + } + } + if (currentShard != null) { + LOG.info("Outputting last shard of size " + + currentShard.sizeInLoci() + ", " + currentShard.approximateSizeInBytes() + " bytes " + + currentShard.contig); + output.output(currentShard.finalize(index, (int)contig.end)); + } + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/ShardingPolicy.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/ShardingPolicy.java new file mode 100644 index 0000000..5a3425b --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/ShardingPolicy.java @@ -0,0 +1,47 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers.bam; + +/** + * Different sharding policies and constants governing + * how we slice the data in BAM file. + */ +public interface ShardingPolicy { + /** + * Decides whether a shard we are growing is large enough to be finalized + * and submitted for processing. + */ + public boolean shardBigEnough(BAMShard shard); + + static final int MAX_BYTES_PER_SHARD = 10*1024*1024; // 10MB + public static ShardingPolicy BYTE_SIZE_POLICY = + new ShardingPolicy() { + @Override + public boolean shardBigEnough(BAMShard shard) { + return shard.approximateSizeInBytes() > MAX_BYTES_PER_SHARD; + } + }; + + static final int MAX_BASE_PAIRS_PER_SHARD = 100000; + public static ShardingPolicy LOCI_SIZE_POLICY = + new ShardingPolicy() { + @Override + public boolean shardBigEnough(BAMShard shard) { + return shard.sizeInLoci() > MAX_BASE_PAIRS_PER_SHARD; + } + }; +} + diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/AnnotationUtils.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/AnnotationUtils.java new file mode 100644 index 0000000..a52adc0 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/AnnotationUtils.java @@ -0,0 +1,156 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import com.google.api.client.util.Preconditions; +import com.google.api.services.genomics.model.Annotation; +import com.google.api.services.genomics.model.TranscriptExon; +import com.google.common.collect.ImmutableMap; +import com.google.common.collect.Range; + +import htsjdk.samtools.util.SequenceUtil; + +import java.util.Map; +import java.util.logging.Logger; + +/** + * Utilities for dealing with genomics {@link Annotation}s. Provides some very + * basic functions for determining the effect of a given mutation on a + * transcript. + */ +public class AnnotationUtils { + private static final Logger LOG = Logger.getLogger(AnnotationUtils.class.getName()); + private static final char STOP = '*'; + private static final Map AMINO_ACIDS = + ImmutableMap.builder() + .put("TTT", 'F').put("TTC", 'F').put("TTA", 'L').put("TTG", 'L') + .put("TCT", 'S').put("TCC", 'S').put("TCA", 'S').put("TCG", 'S') + .put("TAT", 'Y').put("TAC", 'Y').put("TAA", STOP).put("TAG", STOP) + .put("TGT", 'C').put("TGC", 'C').put("TGA", STOP).put("TGG", 'W') + .put("CTT", 'L').put("CTC", 'L').put("CTA", 'L').put("CTG", 'L') + .put("CCT", 'P').put("CCC", 'P').put("CCA", 'P').put("CCG", 'P') + .put("CAT", 'H').put("CAC", 'H').put("CAA", 'Q').put("CAG", 'Q') + .put("CGT", 'R').put("CGC", 'R').put("CGA", 'R').put("CGG", 'R') + .put("ATT", 'I').put("ATC", 'I').put("ATA", 'I').put("ATG", 'M') + .put("ACT", 'T').put("ACC", 'T').put("ACA", 'T').put("ACG", 'T') + .put("AAT", 'N').put("AAC", 'N').put("AAA", 'K').put("AAG", 'K') + .put("AGT", 'S').put("AGC", 'S').put("AGA", 'R').put("AGG", 'R') + .put("GTT", 'V').put("GTC", 'V').put("GTA", 'V').put("GTG", 'V') + .put("GCT", 'A').put("GCC", 'A').put("GCA", 'A').put("GCG", 'A') + .put("GAT", 'D').put("GAC", 'D').put("GAA", 'E').put("GAG", 'E') + .put("GGT", 'G').put("GGC", 'G').put("GGA", 'G').put("GGG", 'G').build(); + + private AnnotationUtils() {} + + /** + * Describes the effect of a given variant on a transcript. Subset of the + * annotations API field {@code VariantAnnotation.effect}. + */ + public enum VariantEffect { SYNONYMOUS_SNP, STOP_GAIN, STOP_LOSS, NONSYNONYMOUS_SNP } + + /** + * Determines the effect of the given allele at the given position within a + * transcript. Currently, this routine is relatively primitive: it only works + * with SNPs and only computes effects on coding regions of the transcript. + * This utility currently does not handle any splice sites well, including + * splice site disruption and codons which span two exons. + * + * @param variantStart 0-based absolute start for the variant. + * @param allele Bases to substitute at {@code variantStart}. + * @param transcript The affected transcript. + * @param transcriptBases The reference bases which span the provided + * {@code transcript}. Must match the exact length of the + * {@code transcript.position}. + * @return The effect of this variant on the given transcript, or null if + * unknown. + */ + public static VariantEffect determineVariantTranscriptEffect( + long variantStart, String allele, Annotation transcript, String transcriptBases) { + long txLen = transcript.getPosition().getEnd() - transcript.getPosition().getStart(); + Preconditions.checkArgument(transcriptBases.length() == txLen, + "transcriptBases must have equal length to the transcript; got " + + transcriptBases.length() + " and " + txLen + ", respectively"); + if (allele.length() != 1) { + LOG.fine("determineVariantTranscriptEffects() only supports SNPs, ignoring " + allele); + return null; + } + if (transcript.getTranscript().getCodingSequence() == null) { + LOG.fine("determineVariantTranscriptEffects() only supports intersection with coding " + + "transcript, ignoring "); + return null; + } + + long variantEnd = variantStart + 1; + Range variantRange = Range.closedOpen(variantStart, variantEnd); + Range codingRange = Range.closedOpen( + transcript.getTranscript().getCodingSequence().getStart(), + transcript.getTranscript().getCodingSequence().getEnd()); + if (Boolean.TRUE.equals(transcript.getPosition().getReverseStrand())) { + allele = SequenceUtil.reverseComplement(allele); + } + for (TranscriptExon exon : transcript.getTranscript().getExons()) { + // For now, only compute effects on variants within the coding region of an exon. + Range exonRange = Range.closedOpen(exon.getStart(), exon.getEnd()); + if (exonRange.isConnected(codingRange) && + exonRange.intersection(codingRange).isConnected(variantRange) && + !exonRange.intersection(codingRange).intersection(variantRange).isEmpty()) { + // Get the bases which correspond to this exon. + int txOffset = transcript.getPosition().getStart().intValue(); + String exonBases = transcriptBases.substring( + exon.getStart().intValue() - txOffset, exon.getEnd().intValue() - txOffset); + int variantExonOffset = (int) (variantStart - exon.getStart()); + + if (Boolean.TRUE.equals(transcript.getPosition().getReverseStrand())) { + // Normalize the offset and bases to 5' -> 3'. + exonBases = SequenceUtil.reverseComplement(exonBases); + variantExonOffset = (int) (exon.getEnd() - variantEnd); + } + + // Determine the indices for the codon which contains this variant. + if (exon.getFrame() == null) { + LOG.fine("exon lacks frame data, cannot determine effect"); + return null; + } + int offsetWithinCodon = (variantExonOffset + exon.getFrame().getValue()) % 3; + int codonExonOffset = variantExonOffset - offsetWithinCodon; + if (codonExonOffset < 0 || exonBases.length() <= codonExonOffset+3) { + LOG.fine("variant codon spans multiple exons, this case is not yet handled"); + return null; + } + String fromCodon = exonBases.substring(codonExonOffset, codonExonOffset+3); + String toCodon = + fromCodon.substring(0, offsetWithinCodon) + allele + + fromCodon.substring(offsetWithinCodon + 1); + return codonChangeToEffect(fromCodon, toCodon); + } + } + return null; + } + + private static VariantEffect codonChangeToEffect(String fromCodon, String toCodon) { + Preconditions.checkArgument(AMINO_ACIDS.containsKey(fromCodon), "no such codon: " + fromCodon); + Preconditions.checkArgument(AMINO_ACIDS.containsKey(toCodon), "no such codon: " + toCodon); + char fromAA = AMINO_ACIDS.get(fromCodon); + char toAA = AMINO_ACIDS.get(toCodon); + if (fromAA == toAA) { + return VariantEffect.SYNONYMOUS_SNP; + } else if (toAA == STOP) { + return VariantEffect.STOP_GAIN; + } else if (fromAA == STOP) { + return VariantEffect.STOP_LOSS; + } else { + return VariantEffect.NONSYNONYMOUS_SNP; + } + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/CallFilters.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/CallFilters.java new file mode 100644 index 0000000..4d95202 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/CallFilters.java @@ -0,0 +1,57 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import com.google.api.services.genomics.model.Call; +import com.google.common.collect.ImmutableList; +import com.google.genomics.v1.Variant; +import com.google.genomics.v1.VariantCall; + +public class CallFilters { + + public static ImmutableList getSamplesWithVariantOfMinGenotype(Variant variant, + int minGenotype) { + ImmutableList.Builder samplesWithVariant = ImmutableList.builder(); + for (VariantCall call : variant.getCallsList()) { + for (int genotype : call.getGenotypeList()) { + if (minGenotype <= genotype) { + // Use a greater than zero test since no-calls are -1 and we + // don't want to count those. + samplesWithVariant.add(call); + break; + } + } + } + return samplesWithVariant.build(); + } + + @Deprecated + public static ImmutableList getSamplesWithVariantOfMinGenotype(com.google.api.services.genomics.model.Variant variant, + int minGenotype) { + ImmutableList.Builder samplesWithVariant = ImmutableList.builder(); + for (Call call : variant.getCalls()) { + for (int genotype : call.getGenotype()) { + if (minGenotype <= genotype) { + // Use a greater than zero test since no-calls are -1 and we + // don't want to count those. + samplesWithVariant.add(call); + break; + } + } + } + return samplesWithVariant.build(); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSHelper.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSHelper.java new file mode 100644 index 0000000..73092cf --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSHelper.java @@ -0,0 +1,207 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import com.google.api.client.auth.oauth2.Credential; +import com.google.api.client.http.HttpHeaders; +import com.google.api.client.http.HttpTransport; +import com.google.api.client.json.JsonFactory; +import com.google.api.client.json.jackson2.JacksonFactory; +import com.google.api.services.storage.Storage; +import com.google.api.services.storage.model.StorageObject; +import com.google.cloud.genomics.utils.CredentialFactory; +import com.google.cloud.genomics.utils.GenomicsFactory; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.common.annotations.VisibleForTesting; +import com.google.common.base.Preconditions; +import com.google.common.collect.Lists; + +import java.io.ByteArrayOutputStream; +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.math.BigInteger; +import java.security.GeneralSecurityException; +import java.util.logging.Level; +import java.util.logging.Logger; + +import javax.annotation.Nullable; + +/** + * A helper class to download from Google Cloud Storage. + */ +public class GCSHelper { + + private static final Logger LOGGER = Logger.getLogger(GCSHelper.class.getName()); + private static final boolean IS_APP_ENGINE = false; + private Storage storage; + + /** + * Global instance of the HTTP transport. + */ + private static HttpTransport httpTransport; + /** + * Global instance of the JSON factory. + */ + private static final JsonFactory JSON_FACTORY = JacksonFactory.getDefaultInstance(); + + + /** + * Connects to storage (this is the preferred way). + * + * @param popts already-filled options. + */ + public GCSHelper(GenomicsOptions popts) throws GeneralSecurityException, IOException { + Preconditions.checkNotNull(popts); + // set up storage object + GenomicsFactory factory = GenomicsFactory.builder(popts.getAppName()) + .build(); + httpTransport = factory.getHttpTransport(); + Storage.Builder builder = new Storage.Builder(httpTransport, JSON_FACTORY, null) + .setApplicationName(popts.getAppName()); + OfflineAuth auth = GenomicsOptions.Methods.getGenomicsAuth(popts); + storage = factory.fromOfflineAuth(builder, auth).build(); + } + + /** + * Connects to storage + * (use this if you're a Dataflow worker, as you don't have access to the clients-secrets.json from there). + * + * @param offlineAuth serialized credentials + */ + public GCSHelper(OfflineAuth offlineAuth) throws GeneralSecurityException, IOException { + Preconditions.checkNotNull(offlineAuth); + // set up storage object + GenomicsFactory factory = GenomicsFactory.builder().build(); + httpTransport = factory.getHttpTransport(); + Storage.Builder builder = new Storage.Builder(httpTransport, JSON_FACTORY, null); + storage = factory.fromOfflineAuth(builder, offlineAuth).build(); + } + + /** + * Connects to storage. + * + * @param appName name of your app + * @param secretsFile path to clients-secrets.json + */ + public GCSHelper(String appName, String secretsFile) throws GeneralSecurityException, IOException { + // cf https://groups.google.com/forum/#!msg/google-genomics-discuss/P9A9odUXwaM/ISdIzOXNS3YJ + GenomicsFactory factory = GenomicsFactory.builder(appName).build(); + httpTransport = factory.getHttpTransport(); + Credential creds = CredentialFactory.getCredentialFromClientSecrets(secretsFile, appName); + Storage.Builder builder = new Storage.Builder(httpTransport, JSON_FACTORY, null) + .setApplicationName(appName); + storage = factory.fromCredential(builder, creds).build(); + } + + @VisibleForTesting + GCSHelper() { + } + + /** + * Get the underlying GCS Storage object, for advanced uses + * (e.g. a download progressbar). + */ + public Storage getStorage() { + return this.storage; + } + + /** + * @param name of the file we're interested in + * @return size of the file, in bytes + * @throws IOException + */ + public long getFileSize(String bucket, String name) throws IOException { + Storage.Objects.Get getObject = storage.objects().get(bucket, name); + StorageObject object = getObject.execute(); + BigInteger size = object.getSize(); + if (size.compareTo(BigInteger.valueOf(Long.MAX_VALUE)) > 0) { + throw new RuntimeException("File size is too big for a long!"); + } + return size.longValue(); + } + + + /** + * Retrieve part of the file. + * + * @throws IOException + */ + public ByteArrayOutputStream getPartialObjectData(String bucket, String fname, long start, long endIncl) throws IOException { + return getPartialObjectData(bucket, fname, start, endIncl, null); + } + + /** + * Retrieve part of the file. + * + * Example thing you may want to do with the result: + * String str = new String( Arrays.copyOfRange(out.toByteArray() ); + * + * @throws IOException + */ + public ByteArrayOutputStream getPartialObjectData(String bucket, String fname, long start, long endIncl, + @Nullable ByteArrayOutputStream optionalOldOutputToReuse) throws IOException { + ByteArrayOutputStream out; + if (null == optionalOldOutputToReuse) { + out = new ByteArrayOutputStream((int) (endIncl - start + 1)); + } else { + out = optionalOldOutputToReuse; + out.reset(); + } + Storage.Objects.Get getObject = storage.objects().get(bucket, fname); + + getObject.setRequestHeaders(new HttpHeaders().setRange( + String.format("bytes=%d-%d", start, endIncl))); + + getObject.getMediaHttpDownloader().setDirectDownloadEnabled(!IS_APP_ENGINE); + getObject.executeMediaAndDownloadTo(out); + + if (out.size() != (endIncl - start + 1)) { + String err = "getPartialObjectData failed! Expected " + (endIncl - start + 1) + " bytes, got " + out.size(); + LOGGER.log(Level.WARNING, err); + throw new IOException(err); + } + + return out; + } + + /** + * Retrieve the whole file (to memory). + * + * @throws IOException + */ + public InputStream getWholeObject(String bucket, String fname) throws IOException { + Storage.Objects.Get getObject = storage.objects().get(bucket, fname); + return getObject.executeMediaAsInputStream(); + } + + /** + * Retrieve the whole file (to a temporary file on disk). + * + * @throws IOException + */ + public File getAsFile(String bucket, String fname) throws IOException { + Storage.Objects.Get request = storage.objects().get(bucket, fname); + File file = File.createTempFile("gcsdownload", "obj"); + try (OutputStream out = new FileOutputStream(file)) { + request.executeMediaAndDownloadTo(out); + } + return file; + } + +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOptions.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOptions.java new file mode 100644 index 0000000..bedbda8 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOptions.java @@ -0,0 +1,140 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import java.util.List; +import java.util.logging.Logger; + +import com.fasterxml.jackson.annotation.JsonIgnore; +import com.google.api.client.googleapis.util.Utils; +import com.google.api.client.http.HttpTransport; +import com.google.api.client.json.JsonFactory; +import com.google.api.services.dataflow.DataflowScopes; +import com.google.api.services.genomics.GenomicsScopes; +import com.google.api.services.storage.Storage; +import com.google.api.services.storage.StorageScopes; +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.DefaultValueFactory; +import com.google.cloud.dataflow.sdk.options.PipelineOptions; +import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.genomics.utils.GenomicsFactory; +import com.google.cloud.genomics.utils.OfflineAuth; +import com.google.common.collect.ImmutableList; + +/** + * Options for pipelines that need to access GCS storage. + * Users must call Methods.initialize to get the credentials set up. + * getStorageClient() provides the GCS storage client. + */ +public interface GCSOptions extends GenomicsOptions { + class HttpTransportFactory implements DefaultValueFactory { + @Override + public HttpTransport create(PipelineOptions options) { + return Utils.getDefaultTransport(); + } + } + + @Default.InstanceFactory(HttpTransportFactory.class) + @JsonIgnore + HttpTransport getTransport(); + + void setTransport(HttpTransport transport); + + class JsonFactoryFactory implements DefaultValueFactory { + @Override + public JsonFactory create(PipelineOptions options) { + return Utils.getDefaultJsonFactory(); + } + } + + @Default.InstanceFactory(JsonFactoryFactory.class) + @JsonIgnore + JsonFactory getJsonFactory(); + + void setJsonFactory(JsonFactory jsonFactory); + + + class ScopesFactory implements DefaultValueFactory> { + @Override + public List create(PipelineOptions options) { + return ImmutableList.builder() + .add(DataflowScopes.USERINFO_EMAIL) + .add(GenomicsScopes.GENOMICS) + .add(StorageScopes.DEVSTORAGE_READ_WRITE) + .build(); + } + } + + @Default.InstanceFactory(ScopesFactory.class) + @JsonIgnore + List getScopes(); + + void setScopes(List scopes); + + class GenomicsFactoryFactory implements DefaultValueFactory { + @Override + public GenomicsFactory create(PipelineOptions options) { + GCSOptions gcsOptions = options.as(GCSOptions.class); + try { + return GenomicsFactory + .builder(gcsOptions.getAppName()) + .setScopes(gcsOptions.getScopes()) + .setHttpTransport(gcsOptions.getTransport()) + .setJsonFactory(gcsOptions.getJsonFactory()) + .build(); + } catch (Exception ex) { + throw new RuntimeException(ex); + } + } + } + + @Default.InstanceFactory(GenomicsFactoryFactory.class) + @JsonIgnore + GenomicsFactory getGenomicsFactory(); + + void setGenomicsFactory(GenomicsFactory factory); + + class Methods { + private static final Logger LOG = Logger.getLogger(GCSOptions.class.getName()); + private Methods() { + } + + public static OfflineAuth createGCSAuth(GCSOptions options) { + return GenomicsOptions.Methods.getGenomicsAuth(options); + } + + public static Storage.Objects createStorageClient( + DoFn.Context context, OfflineAuth auth) { + final GCSOptions gcsOptions = + context.getPipelineOptions().as(GCSOptions.class); + return createStorageClient(gcsOptions, auth); + } + + public static Storage.Objects createStorageClient(GCSOptions gcsOptions, + OfflineAuth auth) { + final Storage.Builder storageBuilder = new Storage.Builder( + gcsOptions.getTransport(), + gcsOptions.getJsonFactory(), + null); + + return gcsOptions.getGenomicsFactory() + .fromOfflineAuth(storageBuilder, auth) + .build() + .objects(); + } + + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOutputOptions.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOutputOptions.java new file mode 100644 index 0000000..43a369c --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOutputOptions.java @@ -0,0 +1,45 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import com.google.api.client.repackaged.com.google.common.base.Strings; +import com.google.cloud.dataflow.sdk.options.Description; +import com.google.cloud.dataflow.sdk.options.Validation; +import com.google.cloud.dataflow.sdk.util.gcsfs.GcsPath; +import com.google.common.base.Preconditions; + +/** + * A common options class for all pipelines that write their analysis results to GCS files. + */ +public interface GCSOutputOptions extends GenomicsOptions { + + public static class Methods { + public static void validateOptions(GCSOutputOptions options) { + try { + // Check that we can parse the path. + GcsPath valid = GcsPath.fromUri(options.getOutput()); + // GcsPath allows for empty bucket or filename, but that doesn't make for a good output file. + Preconditions.checkArgument(!Strings.isNullOrEmpty(valid.getBucket()), "Bucket must be specified"); + Preconditions.checkArgument(!Strings.isNullOrEmpty(valid.getObject()), "Filename prefix must be specified"); + } catch (Exception x) { + Preconditions.checkState(false, "output must be a valid Google Cloud Storage URL (starting with gs://)"); + } + } + } + + @Validation.Required + @Description("Google Cloud Storage path prefix of the files to which to write pipeline output, if applicable.") + String getOutput(); + void setOutput(String output); +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/GenomicsOptions.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/GenomicsOptions.java new file mode 100644 index 0000000..d38d711 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/GenomicsOptions.java @@ -0,0 +1,75 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import java.util.Scanner; + +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.Description; +import com.google.cloud.dataflow.sdk.options.GcsOptions; +import com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner; +import com.google.cloud.genomics.utils.OfflineAuth; + +/** + * Contains pipeline options relevant to the creation of Genomics API clients. + */ +public interface GenomicsOptions extends GcsOptions { + + public static class Methods { + + public static OfflineAuth getGenomicsAuth(GenomicsOptions options) { + if (DirectPipelineRunner.class != options.getRunner() + && null != options.getSecretsFile() + && options.getWarnUserCredential()) { + System.out.println("\nThis pipeline will run on GCE VMs and your user credential will" + + " be used by all Dataflow worker instances. Your credentials may be visible to" + + " others with access to the VMs."); + + System.out.println("Do you want to continue (Y/n)?"); + Scanner kbd = new Scanner(System.in); + String decision; + decision = kbd.nextLine(); + switch(decision) { + case "yes": case "Yes": case "YES": case "y": case "Y": + break; + default: + System.exit(0); + } + } + + if (null != options.getSecretsFile()) { + // User credential will be available on all Dataflow workers. + return new OfflineAuth(options.getGcpCredential()); + } + // This "empty" OfflineAuth will default to the Application + // Default Credential available from whereever it is + // accessed (e.g., locally or on GCE). + return new OfflineAuth(); + } + } + + @Description("Set this option to 'false' to disable the yes/no prompt when running" + + " the pipeline with a user credential.") + @Default.Boolean(true) + boolean getWarnUserCredential(); + + void setWarnUserCredential(boolean warnUserCredential); + + @Description("Specifies number of results to return in a single page of results. " + + "If unspecified, the default page size for the Genomics API is used.") + @Default.Integer(0) + int getPageSize(); + + void setPageSize(int pageSize); +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/PairGenerator.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/PairGenerator.java new file mode 100644 index 0000000..e8b0269 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/PairGenerator.java @@ -0,0 +1,85 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import java.util.Comparator; +import java.util.Iterator; +import java.util.List; +import java.util.RandomAccess; + +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.common.base.Function; +import com.google.common.collect.ContiguousSet; +import com.google.common.collect.DiscreteDomain; +import com.google.common.collect.FluentIterable; +import com.google.common.collect.Iterators; +import com.google.common.collect.Range; + +/** + * Generates all combinations (not permutations) of pairs of the elements in the iterable. + * + * WITHOUT_REPLACEMENT - generate Nchoose2 combinations WITH_REPLACEMENT- generate Nchoose2 + * combinations plus an additional N pairs (one for each element in the list) + */ +public enum PairGenerator { + + WITH_REPLACEMENT(true), WITHOUT_REPLACEMENT(false); + + private final boolean withReplacement; + + private PairGenerator(boolean withReplacement) { + this.withReplacement = withReplacement; + } + + /** + * * Generates all combinations (not permutations) of pairs of the elements in the iterable. + * + * The pairs are often used as keys for results in many n^2 analyses where we end up with + * (n*(n-1))/2 or ((n*(n-1))/2)+n results. + * + * @param list + * @param comparator - used to enforce an order upon the elements within each pair + * @return the pairs + */ + public & RandomAccess> FluentIterable> allPairs( + final L list, final Comparator comparator) { + return FluentIterable.from( + ContiguousSet.create(Range.closedOpen(0, list.size()), DiscreteDomain.integers())) + .transformAndConcat(new Function>>() { + @Override + public Iterable> apply(final Integer i) { + return new Iterable>() { + @Override + public Iterator> iterator() { + int iteratorIndex = i; + if (!withReplacement) { + iteratorIndex++; + } + return Iterators.transform(list.listIterator(iteratorIndex), + new Function>() { + + private final X key = list.get(i); + + @Override + public KV apply(X value) { + boolean swap = 0 < comparator.compare(key, value); + return KV.of(swap ? value : key, swap ? key : value); + } + }); + } + }; + } + }); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/ReadFunctions.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/ReadFunctions.java new file mode 100644 index 0000000..7c865fb --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/ReadFunctions.java @@ -0,0 +1,170 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import java.util.List; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import com.google.cloud.dataflow.sdk.transforms.SerializableFunction; +import com.google.cloud.genomics.dataflow.model.ReadBaseQuality; +import com.google.cloud.genomics.dataflow.model.ReadBaseWithReference; +import com.google.common.collect.ImmutableList; +import com.google.genomics.v1.CigarUnit; +import com.google.genomics.v1.Position; +import com.google.genomics.v1.Read; + +/** + * Utility methods for working with genetic read data. + */ +public class ReadFunctions { + + private static final String UNINITIALIZED_REFERENCE_SEQUENCE = "UNINITIALIZED"; + + /** + * Use the given read to build a list of aligned read and reference base + * information. + * + * @param read The read with the alignment information + * @return read and reference information. For a read without an alignment + * or cigar units, null is returned. + */ + public static List extractReadBases(Read read) { + + // Make sure this read has a valid alignment with Cigar Units + if (!read.hasAlignment() || (read.getAlignment().getCigarCount() == 0)) { + return null; + } + + ImmutableList.Builder bases = ImmutableList.builder(); + + String readSeq = read.getAlignedSequence(); + List readQual = read.getAlignedQualityList(); + String refSeq = UNINITIALIZED_REFERENCE_SEQUENCE; + + int refPosAbsoluteOffset = 0; + int readOffset = 0; + for (CigarUnit unit : read.getAlignment().getCigarList()) { + switch(unit.getOperation()) { + case ALIGNMENT_MATCH: + case SEQUENCE_MISMATCH: + case SEQUENCE_MATCH: + for (int i = 0; i < unit.getOperationLength(); i++) { + String refBase = ""; + if (unit.getOperation().equals(CigarUnit.Operation.SEQUENCE_MATCH)) { + refBase = readSeq.substring(readOffset, readOffset + 1); + } else if (!unit.getReferenceSequence().isEmpty()) { + // try to get the ref sequence from the Cigar unit + refBase = unit.getReferenceSequence().substring(i, i + 1); + } else { + // try to get the ref sequence by fully parsing the MD tag if not already cached + if (refSeq != null && refSeq.equals(UNINITIALIZED_REFERENCE_SEQUENCE)) { + refSeq = com.google.cloud.genomics.utils.grpc.ReadUtils + .inferReferenceSequenceByParsingMdFlag(read); + } + if (refSeq != null) { + refBase = refSeq.substring(readOffset, readOffset + 1); + } + } + String name = read.getAlignment().getPosition().getReferenceName(); + Matcher m = Pattern.compile("^(chr)?(X|Y|([12]?\\d))$").matcher(name); + if (m.matches()) { + name = m.group(m.groupCount() - 1); + } + Position refPosition = Position.newBuilder() + .setReferenceName(name) + .setPosition(read.getAlignment().getPosition().getPosition() + + refPosAbsoluteOffset) + .build(); + bases.add(new ReadBaseWithReference(new ReadBaseQuality( + readSeq.substring(readOffset, readOffset + 1), + readQual.get(readOffset)), + refBase, + refPosition)); + refPosAbsoluteOffset++; + readOffset++; + } + break; + + case PAD: // padding (silent deletion from padded reference) + case CLIP_HARD: // hard clipping (clipped sequences NOT present in seq) + break; + + case CLIP_SOFT: // soft clipping (clipped sequences present in SEQ) + case INSERT: // insertion to the reference + readOffset += unit.getOperationLength(); + break; + + case DELETE: // deletion from the reference + case SKIP: // intron (mRNA-to-genome alignment only) + refPosAbsoluteOffset += unit.getOperationLength(); + break; + + default: + throw new IllegalArgumentException("Illegal cigar code: " + unit.getOperation()); + } + } + + return bases.build(); + } + + /** + * Make sure a read is from a chromosome. + */ + public static final SerializableFunction IS_ON_CHROMOSOME + = new SerializableFunction() { + @Override + public Boolean apply(Read r) { + return Pattern.compile("^(chr)?(X|Y|([12]?\\d))$") + .matcher(r.getAlignment().getPosition().getReferenceName()) + .matches(); + } + }; + + /** + * Make sure a read passed QC. + */ + public static final SerializableFunction IS_NOT_QC_FAILURE + = new SerializableFunction() { + @Override + public Boolean apply(Read r) { + return !r.getFailedVendorQualityChecks(); + } + }; + + /** + * Make sure a read is not a duplicate. + */ + public static final SerializableFunction IS_NOT_DUPLICATE + = new SerializableFunction() { + @Override + public Boolean apply(Read r) { + return !r.getDuplicateFragment(); + } + }; + + /** + * Make sure the read alignment is proper (paired end reads facing each other with acceptable + * fragment size). + */ + public static final SerializableFunction IS_PROPER_PLACEMENT + = new SerializableFunction() { + @Override + public Boolean apply(Read r) { + return r.getProperPlacement(); + } + }; +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/ShardOptions.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/ShardOptions.java new file mode 100644 index 0000000..e8d6ca1 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/ShardOptions.java @@ -0,0 +1,41 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import com.google.cloud.dataflow.sdk.options.Default; +import com.google.cloud.dataflow.sdk.options.Description; + +/** + * A common options class for pipelines that shard by genomic region. + */ +public interface ShardOptions extends GenomicsOptions { + + @Description("By default, variants analyses will be run on BRCA1. Pass this flag to run on all " + + "references present in the dataset. Note that certain jobs such as PCA and IBS " + + "will automatically exclude X and Y chromosomes when this option is true.") + boolean isAllReferences(); + void setAllReferences(boolean allReferences); + + @Description("Comma separated tuples of reference:start:end,... " + + "Defaults to '17:41196311:41277499' for BRCA1.") + @Default.String("17:41196311:41277499") + String getReferences(); + void setReferences(String references); + + @Description("The maximum number of bases per shard.") + @Default.Long(1000000) + long getBasesPerShard(); + void setBasesPerShard(long basesPerShard); + +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/ShardReadsTransform.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/ShardReadsTransform.java new file mode 100644 index 0000000..93eef71 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/ShardReadsTransform.java @@ -0,0 +1,47 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import com.google.api.services.genomics.model.Read; +import com.google.cloud.dataflow.sdk.transforms.GroupByKey; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.transforms.PTransform; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.genomics.utils.Contig; + +import com.google.cloud.genomics.dataflow.functions.KeyReadsFn; + +/* + * Takes a collection of reads and shards them out by Contig. + * Can be used to prepare reads for being written to disk in parallel. + */ +public class ShardReadsTransform extends PTransform, PCollection>>> { + + static public interface Options extends KeyReadsFn.Options {} + + @Override + public PCollection>> apply(PCollection reads) { + return reads + .apply(ParDo.named("KeyReads").of(new KeyReadsFn())) + .apply(GroupByKey.create()); + } + + public static PCollection>> shard(PCollection reads) { + return (new ShardReadsTransform()).apply(reads); + } +} + \ No newline at end of file diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/Solver.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/Solver.java new file mode 100644 index 0000000..785be18 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/Solver.java @@ -0,0 +1,98 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import org.apache.commons.math3.analysis.UnivariateFunction; +import org.apache.commons.math3.geometry.euclidean.oned.Interval; +import org.apache.commons.math3.optim.MaxEval; +import org.apache.commons.math3.optim.MaxIter; +import org.apache.commons.math3.optim.nonlinear.scalar.GoalType; +import org.apache.commons.math3.optim.univariate.BrentOptimizer; +import org.apache.commons.math3.optim.univariate.SearchInterval; +import org.apache.commons.math3.optim.univariate.UnivariateObjectiveFunction; +import org.apache.commons.math3.optim.univariate.UnivariatePointValuePair; + +/** + * Maximize a univariate (likelihood) function. + */ +public class Solver { + + /** + * Runs a grid search for the maximum value of a univariate function. + * + * @param fn the likelihood function to minimize + * @param start lower bound of the interval to search + * @param end upper bound of the interval to search + * @param step grid step size + * @return an Interval bracketing the minimum + */ + static Interval gridSearch(UnivariateFunction fn, double start, + double end, double step) { + double lowMax = start; // lower bound on interval surrounding alphaMax + double alphaMax = start - step; + double likMax = 0.0; + + double lastAlpha = start; + double alpha = start; + while (alpha < end) { + double likelihood = fn.value(alpha); + if (alphaMax < start || likelihood > likMax) { + lowMax = lastAlpha; + alphaMax = alpha; + likMax = likelihood; + } + lastAlpha = alpha; + alpha += step; + } + // make sure we've checked the rightmost endpoint (won't happen if + // end - start is not an integer multiple of step, because of roundoff + // errors, etc) + double likelihood = fn.value(end); + if (likelihood > likMax) { + lowMax = lastAlpha; + alphaMax = end; + likMax = likelihood; + } + return new Interval(lowMax, Math.min(end, alphaMax + step)); + } + + /** + * Maximizes a univariate function using a grid search followed by Brent's algorithm. + * + * @param fn the likelihood function to minimize + * @param gridStart the lower bound for the grid search + * @param gridEnd the upper bound for the grid search + * @param gridStep step size for the grid search + * @param relErr relative error tolerance for Brent's algorithm + * @param absErr absolute error tolerance for Brent's algorithm + * @param maxIter maximum # of iterations to perform in Brent's algorithm + * @param maxEval maximum # of Likelihood function evaluations in Brent's algorithm + * + * @return the value of the parameter that maximizes the function + */ + public static double maximize(UnivariateFunction fn, double gridStart, double gridEnd, + double gridStep, double relErr, double absErr, int maxIter, int maxEval) { + Interval interval = gridSearch(fn, gridStart, gridEnd, gridStep); + BrentOptimizer bo = new BrentOptimizer(relErr, absErr); + UnivariatePointValuePair max = bo.optimize( + new MaxIter(maxIter), + new MaxEval(maxEval), + new SearchInterval(interval.getInf(), interval.getSup()), + new UnivariateObjectiveFunction(fn), + GoalType.MAXIMIZE); + return max.getPoint(); + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/TruncatedOutputStream.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/TruncatedOutputStream.java new file mode 100644 index 0000000..0503d04 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/TruncatedOutputStream.java @@ -0,0 +1,101 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import java.io.FilterOutputStream; +import java.io.IOException; +import java.io.OutputStream; + +/** + * FilterOutputStream that writes all but the last bytesToTruncate bytes to + * the underlying OutputStream. + */ +public class TruncatedOutputStream extends FilterOutputStream { + private byte[] buf; + private int count; + private int bytesToTruncate; + OutputStream os; + + public TruncatedOutputStream(OutputStream os, int bytesToTruncate) { + super(os); + this.os = os; + this.buf = new byte[ Math.max(1024, bytesToTruncate) ]; + this.count = 0; + this.bytesToTruncate = bytesToTruncate; + } + + @Override + public void write(int b) throws IOException { + if (count == buf.length) { + flushBuffer(); + } + buf[count++] = (byte)b; + } + + @Override + public void write(byte[] data) throws IOException { + write(data, 0, data.length); + } + + @Override + public void write(byte[] data, int offset, int length) throws IOException { + flushBuffer(); + int spaceRemaining = buf.length - count; + if (length < spaceRemaining) { + System.arraycopy(data, offset, buf, count, length); + count += length; + } else if (length >= bytesToTruncate) { + // We have more than bytesToTruncate to write, so clear the buffer + // completely, and write all but bytesToTruncate directly to the stream. + os.write(buf, 0, count); + final int bytesToWriteDrirectly = length - bytesToTruncate; + os.write(data, offset, bytesToWriteDrirectly); + System.arraycopy(data, offset + bytesToWriteDrirectly, buf, 0, bytesToTruncate); + count = bytesToTruncate; + } else { + // Need this many of the current bytes to stay in the buffer to ensure we + // have at least bytesToTruncate. + final int keepInBuffer = bytesToTruncate - length; + // Write the rest to the stream. + final int bytesToDumpFromBuffer = count - keepInBuffer; + os.write(buf, 0, bytesToDumpFromBuffer); + System.arraycopy(buf, bytesToDumpFromBuffer, buf, 0, keepInBuffer); + System.arraycopy(data, offset, buf, keepInBuffer, length); + count = bytesToTruncate; + } + } + + @Override + public synchronized void flush() throws IOException { + flushBuffer(); + os.flush(); + } + + @Override + public void close() throws IOException { + flushBuffer(); + os.close(); + } + + private void flushBuffer() throws IOException { + final int bytesWeCanSafelyWrite = count - bytesToTruncate; + if (count > bytesToTruncate) { + os.write(buf, 0, bytesWeCanSafelyWrite); + System.arraycopy(buf, bytesWeCanSafelyWrite, buf, 0, bytesToTruncate); + count = bytesToTruncate; + } + } +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/VariantFunctions.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/VariantFunctions.java new file mode 100644 index 0000000..37aa94c --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/VariantFunctions.java @@ -0,0 +1,78 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import java.util.regex.Pattern; + +import com.google.cloud.dataflow.sdk.transforms.SerializableFunction; +import com.google.cloud.genomics.utils.grpc.VariantUtils; + +/** + * Utility methods for working with genetic variant data. + */ +public class VariantFunctions { + + /** + * Determines whether a variant is called according to the provided filtering, using the notation + * required by the VCF 4.2 standard. This means that the filter field of the variant must + * contain either only "PASS" or ".". + */ + public static final SerializableFunction IS_PASSING + = new SerializableFunction() { + @Override + public Boolean apply(com.google.genomics.v1.Variant v) { + return (v.getFilterCount() == 1) && (v.getFilter(0).equalsIgnoreCase("PASS") + || v.getFilter(0).equalsIgnoreCase(".")); + } + }; + + /** + * Determines whether a Variant is from a chromosome. + */ + public static final SerializableFunction IS_ON_CHROMOSOME + = new SerializableFunction() { + @Override + public Boolean apply(com.google.genomics.v1.Variant v) { + return Pattern.compile("^(chr)?(X|Y|([12]?\\d))$") + .matcher(v.getReferenceName()) + .matches(); + } + }; + + /** + * Determines whether a Variant's quality is the lowest level (Phred score 0). + */ + public static final SerializableFunction + IS_NOT_LOW_QUALITY = new SerializableFunction() { + @Override + public Boolean apply(com.google.genomics.v1.Variant v) { + return (v.getQuality() != 0.0); + } + }; + + /** + * Determines whether a Variant is a SNP with a single alternative base. + * + *

To the output of @link{VariantRatios.IsSnpFn} we add the condition that + * the variant has exactly one alternative base. + */ + public static final SerializableFunction + IS_SINGLE_ALTERNATE_SNP = new SerializableFunction(){ + @Override + public Boolean apply(com.google.genomics.v1.Variant v) { + return (v.getAlternateBasesList().size() == 1) && VariantUtils.IS_SNP.apply(v); + } + }; + +} diff --git a/src/main/java/com/google/cloud/genomics/dataflow/writers/WriteReadsTransform.java b/src/main/java/com/google/cloud/genomics/dataflow/writers/WriteReadsTransform.java new file mode 100644 index 0000000..115d593 --- /dev/null +++ b/src/main/java/com/google/cloud/genomics/dataflow/writers/WriteReadsTransform.java @@ -0,0 +1,126 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.writers; + +import com.google.api.services.genomics.model.Read; + +import com.google.cloud.dataflow.sdk.coders.Coder; +import com.google.cloud.dataflow.sdk.coders.DelegateCoder; +import com.google.cloud.dataflow.sdk.coders.StringUtf8Coder; +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.transforms.Create; +import com.google.cloud.dataflow.sdk.transforms.PTransform; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.transforms.View; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.dataflow.sdk.values.PCollectionTuple; +import com.google.cloud.dataflow.sdk.values.PCollectionView; +import com.google.cloud.dataflow.sdk.values.TupleTag; + +import com.google.cloud.genomics.dataflow.functions.CombineShardsFn; +import com.google.cloud.genomics.dataflow.functions.WriteShardFn; +import com.google.cloud.genomics.dataflow.pipelines.ShardedBAMWriting.HeaderInfo; +import com.google.cloud.genomics.utils.Contig; + +import htsjdk.samtools.SAMTextHeaderCodec; +import htsjdk.samtools.util.StringLineReader; +import htsjdk.samtools.ValidationStringency; + +import java.io.StringWriter; +import java.util.Arrays; + +/* + * Writes sets of reads to BAM files in parallel, then combines the files and writes an index + * for the combined file. + */ +public class WriteReadsTransform extends PTransform> { + + public static interface Options extends WriteShardFn.Options {} + + public static TupleTag>> SHARDED_READS_TAG = new TupleTag<>(); + public static TupleTag HEADER_TAG = new TupleTag<>(); + private String output; + private Pipeline pipeline; + + @Override + public PCollection apply(PCollectionTuple tuple) { + final PCollection header = tuple.get(HEADER_TAG); + final PCollectionView headerView = + header.apply(View.asSingleton()); + + final PCollection>> shardedReads = tuple.get(SHARDED_READS_TAG); + + final PCollection writtenShardNames = + shardedReads.apply(ParDo.named("Write shards") + .withSideInputs(Arrays.asList(headerView)) + .of(new WriteShardFn(headerView))); + + final PCollectionView> writtenShardsView = + writtenShardNames.apply(View.asIterable()); + + final PCollection destinationPath = this.pipeline.apply( + Create.of(this.output)); + + final PCollection writtenFile = destinationPath.apply( + ParDo.named("Combine shards") + .withSideInputs(writtenShardsView) + .of(new CombineShardsFn(writtenShardsView))); + + return writtenFile; + } + + private WriteReadsTransform(String output, Pipeline pipeline) { + this.output = output; + this.pipeline = pipeline; + } + + public static PCollection write(PCollection>> shardedReads, HeaderInfo headerInfo, + String output, Pipeline pipeline) { + final PCollectionTuple tuple = PCollectionTuple + .of(SHARDED_READS_TAG,shardedReads) + .and(HEADER_TAG, pipeline.apply(Create.of(headerInfo).withCoder(HEADER_INFO_CODER))); + return (new WriteReadsTransform(output, pipeline)).apply(tuple); + } + + static Coder HEADER_INFO_CODER = DelegateCoder.of( + StringUtf8Coder.of(), + new DelegateCoder.CodingFunction() { + @Override + public String apply(HeaderInfo info) throws Exception { + final StringWriter stringWriter = new StringWriter(); + SAM_HEADER_CODEC.encode(stringWriter, info.header); + return info.firstShard.toString() + "\n" + stringWriter.toString(); + } + }, + new DelegateCoder.CodingFunction() { + @Override + public HeaderInfo apply(String str) throws Exception { + int newLinePos = str.indexOf("\n"); + String contigStr = str.substring(0, newLinePos); + String headerStr = str.substring(newLinePos + 1); + return new HeaderInfo( + SAM_HEADER_CODEC.decode(new StringLineReader(headerStr), + "HEADER_INFO_CODER"), + Contig.parseContigsFromCommandLine(contigStr).iterator().next()); + } + }); + + static final SAMTextHeaderCodec SAM_HEADER_CODEC = new SAMTextHeaderCodec(); + static { + SAM_HEADER_CODEC.setValidationStringency(ValidationStringency.SILENT); + } +} \ No newline at end of file diff --git a/src/main/java/htsjdk/samtools/BAMBlockWriter.java b/src/main/java/htsjdk/samtools/BAMBlockWriter.java new file mode 100644 index 0000000..1c6fd30 --- /dev/null +++ b/src/main/java/htsjdk/samtools/BAMBlockWriter.java @@ -0,0 +1,30 @@ +package htsjdk.samtools; + +import htsjdk.samtools.BAMFileWriter; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMTextHeaderCodec; + +import java.io.File; +import java.io.OutputStream; +import java.io.StringWriter; + +/** + * Subclass of BAMFileWriter that doesn't write the header (but can be told + * explicitly to write the header on demand). + */ +public class BAMBlockWriter extends BAMFileWriter { + public BAMBlockWriter(final OutputStream os, final File file) { + super(os, file); + } + + protected void writeHeader(String textHeader) { + // Deliberately empty. + } + + public void writeHeader(final SAMFileHeader header) { + final StringWriter headerTextBuffer = new StringWriter(); + new SAMTextHeaderCodec().encode(headerTextBuffer, header); + final String headerText = headerTextBuffer.toString(); + super.writeHeader(headerText); + } +} \ No newline at end of file diff --git a/src/main/java/htsjdk/samtools/BAMFileIndexImpl.java b/src/main/java/htsjdk/samtools/BAMFileIndexImpl.java new file mode 100644 index 0000000..5c17237 --- /dev/null +++ b/src/main/java/htsjdk/samtools/BAMFileIndexImpl.java @@ -0,0 +1,31 @@ +package htsjdk.samtools; + +import java.util.List; + +import htsjdk.samtools.seekablestream.SeekableStream; + +/** + * Dealing with visibility constraints of classes in HTSJDK we need to use. + * Exposes BAM Index bin data we need for sharding calculations. + */ +public class BAMFileIndexImpl extends CachingBAMFileIndex { + private SAMSequenceDictionary mBamDictionary; + public BAMFileIndexImpl(SeekableStream stream, SAMSequenceDictionary dict) { + super(stream, dict); + mBamDictionary = dict; + } + + public Bin getBinData(final int referenceIndex, final int binIndex) { + final BAMIndexContent queryResults = getQueryResults(referenceIndex); + + if(queryResults == null) + return null; + return queryResults.getBins().getBin(binIndex); + } + + public List getChunksOverlapping(final String reference, final int startPos, final int endPos) { + int referenceIndex = mBamDictionary.getSequence(reference).getSequenceIndex(); + final BAMIndexContent queryResults = getQueryResults(referenceIndex); + return queryResults.getChunksOverlapping(startPos, endPos); + } +} diff --git a/src/main/java/htsjdk/samtools/SAMFileSpanImpl.java b/src/main/java/htsjdk/samtools/SAMFileSpanImpl.java new file mode 100644 index 0000000..94f6faf --- /dev/null +++ b/src/main/java/htsjdk/samtools/SAMFileSpanImpl.java @@ -0,0 +1,35 @@ +package htsjdk.samtools; + +import java.util.List; + +/** + * Dealing with visibility constraints of classes in HTSJDK we need to use. + * Allows construction of SAMFileSpan objects and exposes a method + * to calculate approximate size of span in bytes. + */ +public class SAMFileSpanImpl extends BAMFileSpan { + private static final long serialVersionUID = 1L; + private long cachedSize = -1; + + public SAMFileSpanImpl() { + super(); + } + + public SAMFileSpanImpl(final List chunks) { + super(chunks); + } + + private static final double AVERAGE_BAM_COMPRESSION_RATIO = 0.39; + + public long approximateSizeInBytes() { + if (cachedSize < 0) { + cachedSize = 0; + for (Chunk chunk : getChunks()) { + final long chunkSpan = Math.round(((chunk.getChunkEnd()>>16)-(chunk.getChunkStart()>>16))/AVERAGE_BAM_COMPRESSION_RATIO); + final int offsetSpan = (int)((chunk.getChunkEnd()&0xFFFF)-(chunk.getChunkStart()&0xFFFF)); + cachedSize += chunkSpan + offsetSpan; + } + } + return cachedSize; + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/coders/GenericJsonCoderProviderTest.java b/src/test/java/com/google/cloud/genomics/dataflow/coders/GenericJsonCoderProviderTest.java new file mode 100644 index 0000000..f358e98 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/coders/GenericJsonCoderProviderTest.java @@ -0,0 +1,65 @@ +package com.google.cloud.genomics.dataflow.coders; + +import static org.hamcrest.Matchers.allOf; +import static org.hamcrest.Matchers.containsString; +import static org.junit.Assert.assertEquals; + +import java.io.Serializable; + +import org.junit.BeforeClass; +import org.junit.Rule; +import org.junit.Test; +import org.junit.rules.ExpectedException; + +import com.google.cloud.dataflow.sdk.coders.CannotProvideCoderException; +import com.google.cloud.dataflow.sdk.coders.Coder; +import com.google.cloud.dataflow.sdk.coders.CoderRegistry; +import com.google.cloud.dataflow.sdk.coders.Proto2Coder; +import com.google.cloud.dataflow.sdk.coders.SerializableCoder; + +public class GenericJsonCoderProviderTest { + private static CoderRegistry registry; + + private static class NotGenericJsonClass {} + + private static class SerializableClass implements Serializable {} + + @Rule + public ExpectedException thrown = ExpectedException.none(); + + @BeforeClass + public static void setUpBeforeClass() throws Exception { + registry = new CoderRegistry(); + registry.registerStandardCoders(); + registry.setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + } + + @Test + public void testGenericJsonFallbackCoderProvider() throws Exception { + Coder coder = registry.getDefaultCoder(com.google.api.services.genomics.model.Read.class); + assertEquals(coder, GenericJsonCoder.of(com.google.api.services.genomics.model.Read.class)); + } + + @Test + public void testGenericJsonFallbackCoderProviderFallsbackToProto2Coder() throws Exception { + Coder coder = registry.getDefaultCoder(com.google.genomics.v1.Read.class); + assertEquals(coder, Proto2Coder.of(com.google.genomics.v1.Read.class)); + } + + @Test + public void testGenericJsonFallbackCoderProviderFallsbackToSerialiableCoder() throws Exception { + Coder coder = registry.getDefaultCoder(SerializableClass.class); + assertEquals(coder, SerializableCoder.of(SerializableClass.class)); + } + + @Test + public void testGenericJsonFallbackCoderProviderThrows() throws Exception { + thrown.expect(CannotProvideCoderException.class); + thrown.expectMessage(allOf( + containsString(NotGenericJsonClass.class.getCanonicalName()), + containsString("No CoderFactory has been registered"), + containsString("does not have a @DefaultCoder annotation"), + containsString("does not implement GenericJson, Message, or Serializable"))); + Coder coder = registry.getDefaultCoder(NotGenericJsonClass.class); + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/coders/GenericJsonCoderTest.java b/src/test/java/com/google/cloud/genomics/dataflow/coders/GenericJsonCoderTest.java new file mode 100644 index 0000000..4197eb1 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/coders/GenericJsonCoderTest.java @@ -0,0 +1,56 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.coders; + +import static org.junit.Assert.assertTrue; + +import com.google.api.services.genomics.model.Read; +import com.google.cloud.dataflow.sdk.coders.Coder.Context; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; + +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import java.io.ByteArrayInputStream; +import java.io.ByteArrayOutputStream; +import java.io.IOException; +import java.io.InputStream; + +@RunWith(JUnit4.class) +public class GenericJsonCoderTest { + + /** + * Tests what happens when trying to read two concatenated JSON objects using GenericJsonCoder + */ + @Test + public void testCodingInIterable() throws IOException { + Read read = new Read(); + read.setId("TEST_READ_1"); + + GenericJsonCoder coder = GenericJsonCoder.of(Read.class); + ByteArrayOutputStream output = new ByteArrayOutputStream(); + coder.encode(read, output, Context.NESTED); + read.setId("TEST_READ_2"); + coder.encode(read, output, Context.NESTED); + + InputStream input = new ByteArrayInputStream(output.toByteArray()); + Read out = coder.decode(input, Context.NESTED); + assertTrue(out.getId().equals("TEST_READ_1")); + out = coder.decode(input, Context.NESTED); + assertTrue(out.getId().equals("TEST_READ_2")); + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/functions/AlleleSimilarityCalculatorTest.java b/src/test/java/com/google/cloud/genomics/dataflow/functions/AlleleSimilarityCalculatorTest.java new file mode 100644 index 0000000..0da2973 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/functions/AlleleSimilarityCalculatorTest.java @@ -0,0 +1,108 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertThat; +import static org.junit.Assert.assertTrue; + +import java.util.List; + +import org.hamcrest.CoreMatchers; +import org.junit.Test; + +import com.google.cloud.dataflow.sdk.transforms.DoFnTester; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.genomics.dataflow.utils.DataUtils; +import com.google.genomics.v1.Variant; + +public class AlleleSimilarityCalculatorTest { + + static final Variant snp1 = Variant.newBuilder() + .setReferenceName("chr7") + .setStart(200019) + .setEnd(200020) + .setReferenceBases("T") + .addAlternateBases("G") + .addCalls(DataUtils.makeVariantCall("het-alt sample", 1, 0)) + .addCalls(DataUtils.makeVariantCall("hom-alt sample", 1, 1)) + .addCalls(DataUtils.makeVariantCall("hom-ref sample", 0, 0)) + .addCalls(DataUtils.makeVariantCall("hom-nocall sample", -1, -1)) + .addCalls(DataUtils.makeVariantCall("ref-nocall sample", -1, 0)) + .build(); + + static final Variant snp2 = Variant.newBuilder() + .setReferenceName("chr7") + .setStart(200020) + .setEnd(200021) + .setReferenceBases("C") + .addAlternateBases("A") + .addCalls(DataUtils.makeVariantCall("hom-alt sample", 1, 1)) + .addCalls(DataUtils.makeVariantCall("het-alt sample", 0, 1)) + .addCalls(DataUtils.makeVariantCall("ref-nocall sample", 0, -1)) + .build(); + + @Test + public void testIsReferenceMajor() { + assertTrue(AlleleSimilarityCalculator.isReferenceMajor(snp1)); + assertFalse(AlleleSimilarityCalculator.isReferenceMajor(snp2)); + } + + @Test + public void testGetSamplesWithVariant() { + assertEquals(4, AlleleSimilarityCalculator.getSamplesWithVariant(snp1).size()); + assertEquals(3, AlleleSimilarityCalculator.getSamplesWithVariant(snp2).size()); + } + + @Test + public void testSharedMinorAllSimilarityFn() { + + CallSimilarityCalculatorFactory fac = new SharedMinorAllelesCalculatorFactory(); + DoFnTester, KV>> simFn = + DoFnTester.of(new AlleleSimilarityCalculator(fac)); + + List, KV>> outputSnp1 = simFn.processBatch(snp1); + assertEquals(6, outputSnp1.size()); + assertThat(outputSnp1, CoreMatchers.hasItems( + KV.of(KV.of("het-alt sample", "ref-nocall sample"), KV.of(0.0, 1)), + KV.of(KV.of("het-alt sample", "hom-ref sample"), KV.of(0.0, 1)), + KV.of(KV.of("het-alt sample", "hom-alt sample"), KV.of(1.0, 1)), + KV.of(KV.of("hom-ref sample", "ref-nocall sample"), KV.of(0.0, 1)), + KV.of(KV.of("hom-alt sample", "ref-nocall sample"), KV.of(0.0, 1)), + KV.of(KV.of("hom-alt sample", "hom-ref sample"), KV.of(0.0, 1)))); + + List, KV>> outputSnp2 = simFn.processBatch(snp2); + assertEquals(3, outputSnp2.size()); + assertThat( + outputSnp2, + CoreMatchers.hasItems(KV.of(KV.of("het-alt sample", "hom-alt sample"), KV.of(0.0, 1)), + KV.of(KV.of("het-alt sample", "ref-nocall sample"), KV.of(1.0, 1)), + KV.of(KV.of("hom-alt sample", "ref-nocall sample"), KV.of(0.0, 1)))); + + Variant[] input = new Variant[] {snp1, snp2}; + List, KV>> outputBoth = simFn.processBatch(input); + assertEquals(6, outputBoth.size()); + assertThat(outputBoth, CoreMatchers.hasItems( + KV.of(KV.of("het-alt sample", "ref-nocall sample"), KV.of(1.0, 2)), + KV.of(KV.of("het-alt sample", "hom-ref sample"), KV.of(0.0, 1)), + KV.of(KV.of("het-alt sample", "hom-alt sample"), KV.of(1.0, 2)), + KV.of(KV.of("hom-ref sample", "ref-nocall sample"), KV.of(0.0, 1)), + KV.of(KV.of("hom-alt sample", "ref-nocall sample"), KV.of(0.0, 2)), + KV.of(KV.of("hom-alt sample", "hom-ref sample"), KV.of(0.0, 1)))); + + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/functions/CallSimilarityCalculatorTest.java b/src/test/java/com/google/cloud/genomics/dataflow/functions/CallSimilarityCalculatorTest.java new file mode 100644 index 0000000..df54992 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/functions/CallSimilarityCalculatorTest.java @@ -0,0 +1,162 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import static com.google.common.collect.Lists.newArrayList; +import static com.google.common.collect.Maps.newHashMap; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; + +import java.util.List; +import java.util.Map; + +import org.junit.Before; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import com.google.cloud.dataflow.sdk.transforms.DoFnTester; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.genomics.dataflow.utils.DataUtils; +import com.google.genomics.v1.Variant; +import com.google.genomics.v1.VariantCall; + +@RunWith(JUnit4.class) +public class CallSimilarityCalculatorTest { + + private static final double DELTA = 1e-6; + + private List calls = newArrayList(); + + private List variants = newArrayList(); + + private static final String H1 = "H1"; + + private static final String H2 = "H2"; + + private static final String H3 = "H3"; + + @Before + public void setUp() { + calls.add(DataUtils.makeVariantCall(H1, 0, 0)); + calls.add(DataUtils.makeVariantCall(H2, 1, 0)); + calls.add(DataUtils.makeVariantCall(H3, 0, 1)); + calls.add(DataUtils.makeVariantCall(H2, 1, 1)); + calls.add(DataUtils.makeVariantCall(H3, 1, 1)); + calls.add(DataUtils.makeVariantCall(H2, 1)); + calls.add(DataUtils.makeVariantCall(H3, 0)); + calls.add(DataUtils.makeVariantCall(H2, 1, 0, 1)); + calls.add(DataUtils.makeVariantCall(H3, 1, 0, 0)); + + variants.add(Variant.newBuilder().addCalls(calls.get(0)).addCalls(calls.get(1)).addCalls(calls.get(2)).build()); + variants.add(Variant.newBuilder().addCalls(calls.get(0)).addCalls(calls.get(3)).addCalls(calls.get(4)).build()); + variants.add(Variant.newBuilder().addCalls(calls.get(0)).addCalls(calls.get(5)).addCalls(calls.get(6)).build()); + variants.add(Variant.newBuilder().addCalls(calls.get(0)).addCalls(calls.get(7)).addCalls(calls.get(8)).build()); + } + + @Test + public void testSharedAllelesRatioCalculator() { + CallSimilarityCalculator calculator = new SharedAllelesRatioCalculator(); + + assertEquals(0.5, calculator.similarity(calls.get(0), calls.get(1)), DELTA); + assertEquals(0, calculator.similarity(calls.get(0), calls.get(4)), DELTA); + assertEquals(0.5, calculator.similarity(calls.get(3), calls.get(2)), DELTA); + assertEquals(1, calculator.similarity(calls.get(3), calls.get(4)), DELTA); + assertEquals(0.5, calculator.similarity(calls.get(4), calls.get(5)), DELTA); + assertEquals(1.0 / 3.0, calculator.similarity(calls.get(5), calls.get(7)), DELTA); + assertEquals(2.0 / 3.0, calculator.similarity(calls.get(7), calls.get(8)), DELTA); + assertEquals(0, calculator.similarity(calls.get(6), calls.get(7)), DELTA); + } + + @Test + public void testIsReferenceMajor() { + assertTrue(AlleleSimilarityCalculator.isReferenceMajor(variants.get(0))); + assertFalse(AlleleSimilarityCalculator.isReferenceMajor(variants.get(1))); + assertTrue(AlleleSimilarityCalculator.isReferenceMajor(variants.get(2))); + assertTrue(AlleleSimilarityCalculator.isReferenceMajor(variants.get(3))); + } + + @Test + public void testSharedMinorAllelesCalculatorWhenReferenceIsMinor() { + CallSimilarityCalculator calculator = new SharedMinorAllelesCalculator(false); + + assertEquals(1, calculator.similarity(calls.get(0), calls.get(1)), DELTA); + assertEquals(0, calculator.similarity(calls.get(0), calls.get(4)), DELTA); + assertEquals(0, calculator.similarity(calls.get(3), calls.get(2)), DELTA); + assertEquals(0, calculator.similarity(calls.get(3), calls.get(4)), DELTA); + assertEquals(0, calculator.similarity(calls.get(4), calls.get(5)), DELTA); + assertEquals(1, calculator.similarity(calls.get(5), calls.get(7)), DELTA); + assertEquals(1, calculator.similarity(calls.get(7), calls.get(8)), DELTA); + assertEquals(1, calculator.similarity(calls.get(6), calls.get(7)), DELTA); + } + + @Test + public void testSharedMinorAllelesCalculatorWhenReferenceIsMajor() { + CallSimilarityCalculator calculator = new SharedMinorAllelesCalculator(true); + + assertEquals(0, calculator.similarity(calls.get(0), calls.get(1)), DELTA); + assertEquals(0, calculator.similarity(calls.get(0), calls.get(4)), DELTA); + assertEquals(1, calculator.similarity(calls.get(3), calls.get(2)), DELTA); + assertEquals(1, calculator.similarity(calls.get(3), calls.get(4)), DELTA); + assertEquals(1, calculator.similarity(calls.get(4), calls.get(5)), DELTA); + assertEquals(1, calculator.similarity(calls.get(5), calls.get(7)), DELTA); + assertEquals(1, calculator.similarity(calls.get(7), calls.get(8)), DELTA); + assertEquals(0, calculator.similarity(calls.get(6), calls.get(7)), DELTA); + } + + @Test + public void testAlleleSimilarityCalculatorWithSharedAllelesRatio() { + Map, KV> fnOutputMap = + calculatorOutputAsMap(new SharedAllelesRatioCalculatorFactory()); + + assertEquals(fnOutputMap.get(KV.of(H1, H2)).getKey(), 0.5 + 1.0 / 3.0, DELTA); + assertEquals(fnOutputMap.get(KV.of(H1, H3)).getKey(), 1.0 + 1.0 / 3.0, DELTA); + assertEquals(fnOutputMap.get(KV.of(H2, H3)).getKey(), 1.0 + 2.0 / 3.0, DELTA); + + assertEquals(4, fnOutputMap.get(KV.of(H1, H2)).getValue().intValue()); + assertEquals(4, fnOutputMap.get(KV.of(H1, H3)).getValue().intValue()); + assertEquals(4, fnOutputMap.get(KV.of(H2, H3)).getValue().intValue()); + } + + @Test + public void testAlleleSimilarityCalculatorWithSharedMinorAlleles() { + Map, KV> fnOutputMap = + calculatorOutputAsMap(new SharedMinorAllelesCalculatorFactory()); + + assertEquals(0.0, fnOutputMap.get(KV.of(H1, H2)).getKey(), DELTA); + assertEquals(0.0, fnOutputMap.get(KV.of(H1, H3)).getKey(), DELTA); + assertEquals(2.0, fnOutputMap.get(KV.of(H2, H3)).getKey(), DELTA); + + assertEquals(4, fnOutputMap.get(KV.of(H1, H2)).getValue().intValue()); + assertEquals(4, fnOutputMap.get(KV.of(H1, H3)).getValue().intValue()); + assertEquals(4, fnOutputMap.get(KV.of(H2, H3)).getValue().intValue()); + } + + private Map, KV> calculatorOutputAsMap( + CallSimilarityCalculatorFactory calculatorFactory) { + DoFnTester, KV>> fnTester = + DoFnTester.of(new AlleleSimilarityCalculator(calculatorFactory)); + List, KV>> fnOutput = + fnTester.processBatch(variants.toArray(new Variant[] {})); + Map, KV> fnOutputMap = newHashMap(); + for (KV, KV> kv : fnOutput) { + fnOutputMap.put(kv.getKey(), kv.getValue()); + } + return fnOutputMap; + } + +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/functions/ExtractSimilarCallsetsTest.java b/src/test/java/com/google/cloud/genomics/dataflow/functions/ExtractSimilarCallsetsTest.java new file mode 100644 index 0000000..c6fa513 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/functions/ExtractSimilarCallsetsTest.java @@ -0,0 +1,82 @@ +/* +Copyright 2014 Google Inc. All rights reserved. + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. +*/ +package com.google.cloud.genomics.dataflow.functions; + +import static org.junit.Assert.assertEquals; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; + +import org.junit.Before; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import com.google.api.services.genomics.model.Call; +import com.google.cloud.genomics.dataflow.utils.DataUtils; +import com.google.common.collect.BiMap; +import com.google.common.collect.HashBiMap; +import com.google.genomics.v1.Variant; +import com.google.genomics.v1.VariantCall; + +@RunWith(JUnit4.class) +public class ExtractSimilarCallsetsTest { + + @Test + public void testGetSamplesWithVariant() throws Exception { + ExtractSimilarCallsets.v1 doFn = new ExtractSimilarCallsets.v1(); + + Variant variant = Variant.newBuilder().build(); + assertEquals(Collections.emptyList(), doFn.getSamplesWithVariant(variant)); + + VariantCall ref = DataUtils.makeVariantCall("ref", 0, 0); + variant = Variant.newBuilder().addCalls(ref).build(); + assertEquals(Collections.emptyList(), doFn.getSamplesWithVariant(variant)); + + VariantCall alt1 = DataUtils.makeVariantCall("alt1", 1, 0); + variant = Variant.newBuilder().addCalls(ref).addCalls(alt1).build(); + assertEquals(Collections.singletonList("alt1"), doFn.getSamplesWithVariant(variant)); + + VariantCall alt2 = DataUtils.makeVariantCall("alt2", 0, 1); + VariantCall alt3 = DataUtils.makeVariantCall("alt3", 1, 1); + variant = Variant.newBuilder().addCalls(ref) + .addCalls(alt1).addCalls(alt2).addCalls(alt3).build(); + assertEquals(Arrays.asList("alt1", "alt2", "alt3"), doFn.getSamplesWithVariant(variant)); + } + + @Test + public void testGetSamplesWithVariantv1beta2() throws Exception { + ExtractSimilarCallsets.v1beta2 doFn = new ExtractSimilarCallsets.v1beta2(); + + com.google.api.services.genomics.model.Variant variant = new com.google.api.services.genomics.model.Variant(); + List calls = new ArrayList(); + + variant.setCalls(calls); + assertEquals(Collections.emptyList(), doFn.getSamplesWithVariant(variant)); + + calls.add(DataUtils.makeCall("ref", 0, 0)); + assertEquals(Collections.emptyList(), doFn.getSamplesWithVariant(variant)); + + calls.add(DataUtils.makeCall("alt1", 1, 0)); + assertEquals(Collections.singletonList("alt1"), doFn.getSamplesWithVariant(variant)); + + calls.add(DataUtils.makeCall("alt2", 0, 1)); + calls.add(DataUtils.makeCall("alt3", 1, 1)); + assertEquals(Arrays.asList("alt1", "alt2", "alt3"), doFn.getSamplesWithVariant(variant)); + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/functions/LikelihoodFnTest.java b/src/test/java/com/google/cloud/genomics/dataflow/functions/LikelihoodFnTest.java new file mode 100644 index 0000000..68e7278 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/functions/LikelihoodFnTest.java @@ -0,0 +1,134 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.functions; + +import com.google.cloud.genomics.dataflow.model.ReadCounts; +import com.google.cloud.genomics.dataflow.model.ReadQualityCount; +import com.google.cloud.genomics.dataflow.model.ReadQualityCount.Base; +import com.google.common.collect.ImmutableMap; +import com.google.genomics.v1.Position; + +import junit.framework.TestCase; + +import org.apache.commons.math3.util.Precision; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import java.util.Map; + +/** + * Unit tests for {@link LikelihoodFn}. + */ +@RunWith(JUnit4.class) +public class LikelihoodFnTest extends TestCase { + + @Test + public void testValue() { + final double tolerance = 0.0000001; // slop factor for floating point comparisons + final double alpha = 0.25; + final int errPhred = 10; // P(err) = 0.1 + final double pRef = 0.6; + + Position position1 = Position.newBuilder() + .setReferenceName("1") + .setPosition(123L) + .build(); + + /* + * Observe single REF read + */ + ImmutableMap.Builder countsBuilder + = ImmutableMap.builder(); + ReadCounts rc = new ReadCounts(); + rc.setRefFreq(pRef); + ReadQualityCount rqc = new ReadQualityCount(); + rqc.setBase(Base.REF); + rqc.setQuality(errPhred); + rqc.setCount(1); + rc.addReadQualityCount(rqc); + countsBuilder.put(position1, rc); + Map readCounts = countsBuilder.build(); + LikelihoodFn fn = new LikelihoodFn(readCounts); + // Likelihood of a single REF with the parameters above + final double likRef = 0.3354133333; + assertEquals(Precision.compareTo(fn.value(alpha), Math.log(likRef), tolerance), 0); + + /* + * Observe single NONREF read + */ + countsBuilder = ImmutableMap.builder(); + rc = new ReadCounts(); + rc.setRefFreq(pRef); + rqc = new ReadQualityCount(); + rqc.setBase(Base.NONREF); + rqc.setQuality(errPhred); + rqc.setCount(1); + rc.addReadQualityCount(rqc); + countsBuilder.put(position1, rc); + readCounts = countsBuilder.build(); + fn = new LikelihoodFn(readCounts); + // Likelihood of a single NONREF with the parameters above + final double likNonref = 0.20368; + assertEquals(Precision.compareTo(fn.value(alpha), Math.log(likNonref), tolerance), 0); + + /* + * Observe single OTHER read + */ + countsBuilder = ImmutableMap.builder(); + rc = new ReadCounts(); + rc.setRefFreq(pRef); + rqc = new ReadQualityCount(); + rqc.setBase(Base.OTHER); + rqc.setQuality(errPhred); + rqc.setCount(1); + rc.addReadQualityCount(rqc); + countsBuilder.put(position1, rc); + readCounts = countsBuilder.build(); + fn = new LikelihoodFn(readCounts); + // Likelihood of a single OTHER with the parameters above + final double likOther = 0.03850666667; + assertEquals(Precision.compareTo(fn.value(alpha), Math.log(likOther), tolerance), 0); + + // Likelihood for reads at 2 different positions should be product of + // likelihoods for individual reads + Position position2 = Position.newBuilder() + .setReferenceName("1") + .setPosition(124L) + .build(); + countsBuilder = ImmutableMap.builder(); + rc = new ReadCounts(); + rc.setRefFreq(pRef); + rqc = new ReadQualityCount(); + rqc.setBase(Base.REF); + rqc.setQuality(errPhred); + rqc.setCount(1); + rc.addReadQualityCount(rqc); + countsBuilder.put(position1, rc); + rc = new ReadCounts(); + rc.setRefFreq(pRef); + rqc = new ReadQualityCount(); + rqc.setBase(Base.NONREF); + rqc.setQuality(errPhred); + rqc.setCount(1); + rc.addReadQualityCount(rqc); + countsBuilder.put(position2, rc); + readCounts = countsBuilder.build(); + fn = new LikelihoodFn(readCounts); + assertEquals(Precision.compareTo(fn.value(alpha), Math.log(likRef * likNonref), + tolerance), 0); + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/functions/grpc/JoinNonVariantSegmentsWithVariantsTest.java b/src/test/java/com/google/cloud/genomics/dataflow/functions/grpc/JoinNonVariantSegmentsWithVariantsTest.java new file mode 100644 index 0000000..c9410f9 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/functions/grpc/JoinNonVariantSegmentsWithVariantsTest.java @@ -0,0 +1,204 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.functions.grpc; + +import static com.google.common.collect.Lists.newArrayList; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertThat; +import static org.junit.Assert.assertTrue; + +import java.util.Comparator; +import java.util.List; + +import org.hamcrest.CoreMatchers; +import org.hamcrest.collection.IsIterableWithSize; +import org.junit.Before; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.testing.DataflowAssert; +import com.google.cloud.dataflow.sdk.testing.TestPipeline; +import com.google.cloud.dataflow.sdk.transforms.Create; +import com.google.cloud.dataflow.sdk.transforms.DoFnTester; +import com.google.cloud.dataflow.sdk.transforms.GroupByKey; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.transforms.SerializableFunction; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.genomics.dataflow.functions.grpc.JoinNonVariantSegmentsWithVariants; +import com.google.common.collect.Lists; +import com.google.genomics.v1.Variant; +import com.google.genomics.v1.VariantCall; + +@RunWith(JUnit4.class) +public class JoinNonVariantSegmentsWithVariantsTest { + + private static final List variantCalls = Lists.newArrayList(VariantCall.newBuilder() + .setCallSetName("het-alt sample").addGenotype(1).addGenotype(0).build(), VariantCall + .newBuilder().setCallSetName("hom-alt sample").addGenotype(1).addGenotype(1).build()); + + private static final List blockRecord1Calls = Lists.newArrayList(VariantCall + .newBuilder().setCallSetName("hom sample").addGenotype(0).addGenotype(0).build(), VariantCall + .newBuilder().setCallSetName("no call sample").addGenotype(-1).addGenotype(-1).build()); + + private static final List blockRecord2Calls = Lists.newArrayList(VariantCall + .newBuilder().setCallSetName("hom no-call sample").addGenotype(-1).addGenotype(0).build()); + + private static final Variant expectedSnp1 = Variant.newBuilder().setReferenceName("chr7") + .setStart(200010).setEnd(200011).setReferenceBases("A").addAlternateBases("C") + .addAllCalls(variantCalls).addAllCalls(blockRecord1Calls).build(); + + private static final Variant expectedSnp2 = Variant.newBuilder().setReferenceName("chr7") + .setStart(200019).setEnd(200020).setReferenceBases("T").addAlternateBases("G") + .addAllCalls(variantCalls).addAllCalls(blockRecord1Calls).addAllCalls(blockRecord2Calls) + .build(); + + private static final Variant expectedInsert = Variant.newBuilder().setReferenceName("chr7") + .setStart(200010).setEnd(200011).setReferenceBases("A").addAlternateBases("AC") + .addAllCalls(variantCalls).build(); + + private Variant snp1; + private Variant snp2; + private Variant insert; + private Variant blockRecord1; + private Variant blockRecord2; + private Variant[] input; + + @Before + public void setUp() { + snp1 = + Variant.newBuilder().setReferenceName("chr7").setStart(200010).setEnd(200011) + .setReferenceBases("A").addAlternateBases("C").addAllCalls(variantCalls).build(); + + snp2 = + Variant.newBuilder().setReferenceName("chr7").setStart(200019).setEnd(200020) + .setReferenceBases("T").addAlternateBases("G").addAllCalls(variantCalls).build(); + + insert = + Variant.newBuilder().setReferenceName("chr7").setStart(200010).setEnd(200011) + .setReferenceBases("A").addAlternateBases("AC").addAllCalls(variantCalls).build(); + + blockRecord1 = + Variant.newBuilder().setReferenceName("chr7").setStart(199005).setEnd(202050) + .setReferenceBases("A").addAllCalls(blockRecord1Calls).build(); + + blockRecord2 = + Variant.newBuilder().setReferenceName("chr7").setStart(200011).setEnd(200020) + .setReferenceBases("A").addAllCalls(blockRecord2Calls).build(); + + input = new Variant[] {snp1, snp2, insert, blockRecord1, blockRecord2}; + } + + @Test + public void testVariantVariantComparator() { + Comparator comparator = JoinNonVariantSegmentsWithVariants.NON_VARIANT_SEGMENT_COMPARATOR; + + assertEquals(-1, comparator.compare(blockRecord1, snp1)); + assertEquals(1, comparator.compare(blockRecord2, snp1)); + assertEquals(-1, comparator.compare(snp1, snp2)); + + // Two variants at the same location + Variant snp1DifferentAlt = + Variant.newBuilder(snp1) + .clearAlternateBases() + .addAlternateBases("G") + .build(); + assertTrue(0 > comparator.compare(snp1, snp1DifferentAlt)); + + // Block record and variant at the same location + Variant blockRecordForSnp1 = + Variant.newBuilder(snp1) + .clearAlternateBases() + .build(); + assertEquals(1, comparator.compare(snp1, blockRecordForSnp1)); + + List variants = newArrayList(input); + variants.add(snp1DifferentAlt); + variants.add(blockRecordForSnp1); + + // Check all permutations + for (Variant v1 : variants) { + for (Variant v2 : variants) { + assertTrue(Integer.signum(comparator.compare(v1, v2)) == -Integer.signum(comparator + .compare(v2, v1))); + } + } + } + + @Test + public void testIsOverlapping() { + assertTrue(JoinNonVariantSegmentsWithVariants.isOverlapping(blockRecord1, snp1)); + assertTrue(JoinNonVariantSegmentsWithVariants.isOverlapping(blockRecord1, snp2)); + assertFalse(JoinNonVariantSegmentsWithVariants.isOverlapping(blockRecord2, snp1)); + assertTrue(JoinNonVariantSegmentsWithVariants.isOverlapping(blockRecord2, snp2)); + } + + @Test + public void testBinVariantsFn() { + + DoFnTester, Variant>> binVariantsFn = + DoFnTester.of(new JoinNonVariantSegmentsWithVariants.BinVariants()); + + List, Variant>> binVariantsOutput = binVariantsFn.processBatch(input); + assertThat(binVariantsOutput, CoreMatchers.hasItem(KV.of(KV.of("chr7", 200L), snp1))); + assertThat(binVariantsOutput, CoreMatchers.hasItem(KV.of(KV.of("chr7", 200L), snp2))); + assertThat(binVariantsOutput, CoreMatchers.hasItem(KV.of(KV.of("chr7", 200L), insert))); + assertThat(binVariantsOutput, CoreMatchers.hasItem(KV.of(KV.of("chr7", 199L), blockRecord1))); + assertThat(binVariantsOutput, CoreMatchers.hasItem(KV.of(KV.of("chr7", 200L), blockRecord1))); + assertThat(binVariantsOutput, CoreMatchers.hasItem(KV.of(KV.of("chr7", 201L), blockRecord1))); + assertThat(binVariantsOutput, CoreMatchers.hasItem(KV.of(KV.of("chr7", 202L), blockRecord1))); + assertThat(binVariantsOutput, CoreMatchers.hasItem(KV.of(KV.of("chr7", 200L), blockRecord2))); + assertEquals(8, binVariantsOutput.size()); + } + + @Test + public void testJoinVariantsPipeline() { + + Pipeline p = TestPipeline.create(); + + PCollection inputVariants = + p.apply(Create.of(input)); + + PCollection, Variant>> binnedVariants = + inputVariants.apply(ParDo.of(new JoinNonVariantSegmentsWithVariants.BinVariants())); + + PCollection, Iterable>> groupedBinnedVariants = + binnedVariants.apply(GroupByKey., Variant>create()); + + PCollection mergedVariants = + groupedBinnedVariants.apply(ParDo.of(new JoinNonVariantSegmentsWithVariants.MergeVariants())); + + DataflowAssert.that(mergedVariants).satisfies( + new AssertThatHasExpectedContentsForTestJoinVariants()); + + p.run(); + } + + static class AssertThatHasExpectedContentsForTestJoinVariants implements + SerializableFunction, Void> { + + @Override + public Void apply(Iterable actual) { + assertThat(actual, CoreMatchers.hasItem(expectedSnp1)); + assertThat(actual, CoreMatchers.hasItem(expectedSnp2)); + assertThat(actual, CoreMatchers.hasItem(expectedInsert)); + assertThat(actual, IsIterableWithSize.iterableWithSize(3)); + + return null; + } + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/pipelines/CalculateCoverageTest.java b/src/test/java/com/google/cloud/genomics/dataflow/pipelines/CalculateCoverageTest.java new file mode 100644 index 0000000..13bd8a8 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/pipelines/CalculateCoverageTest.java @@ -0,0 +1,296 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import com.google.api.services.genomics.model.Annotation; +import com.google.api.services.genomics.model.Position; +import com.google.api.services.genomics.model.RangePosition; +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.dataflow.sdk.testing.DataflowAssert; +import com.google.cloud.dataflow.sdk.testing.TestPipeline; +import com.google.cloud.dataflow.sdk.transforms.Create; +import com.google.cloud.dataflow.sdk.transforms.GroupByKey; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import com.google.cloud.genomics.dataflow.model.PosRgsMq; +import com.google.cloud.genomics.dataflow.pipelines.CalculateCoverage.CalculateCoverageMean; +import com.google.cloud.genomics.dataflow.pipelines.CalculateCoverage.CalculateQuantiles; +import com.google.common.collect.Lists; +import com.google.genomics.v1.CigarUnit; +import com.google.genomics.v1.CigarUnit.Operation; +import com.google.genomics.v1.LinearAlignment; +import com.google.genomics.v1.Read; + +import org.junit.BeforeClass; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; + +/** + * Class for testing the Calculate Coverage class + */ +@RunWith(JUnit4.class) +public class CalculateCoverageTest { + + private static List testSet; + private static List> testSet2; + // The bucket width we are calculating coverage for. + static final int TEST_BUCKET_WIDTH = 2; + // The number of quantiles are are computing. + static final int TEST_NUM_QUANTILES = 3; + // The input data, see setup + static List input; + // Input read position info + static final long[] readPosInfo = {0, 1, 2, 0, 0, 0, 0, 2, 3, 0, 0, 0, 3, 2, 0, + 0, 0, 0, 1, 3, 0, 0, 1, 0, 2}; + // Input read mapping quality info, (L = 5, M = 15, H = 35) + static final int[] readMQInfo = {5, 15, 35, 15, 35, 5, 5, 15, 15, 35, 5, 15, 35, 35, 15, + 5, 15, 15, 35, 35, 5, 5, 5, 5, 5}; + // Input read length info + static final int[] readLengthInfo = {4, 3, 1, 3, 1, 4, 3, 2, 1, 1, 4, 2, 1, 1, 3, + 4, 2, 1, 2, 1, 4, 3, 3, 2, 1}; + + static final Operation[] ops1 = {Operation.INSERT, Operation.SEQUENCE_MISMATCH, Operation.PAD}; + static final Operation[] ops2 = {Operation.DELETE, Operation.SKIP, Operation.SEQUENCE_MATCH}; + static final Operation[] ops3 = + {Operation.INSERT, Operation.ALIGNMENT_MATCH, Operation.CLIP_SOFT}; + + @BeforeClass + public static void oneTimeSetUp() { + // Test data for testCalculateCoverageMean + // Read 1 (Contains two operations that result in increasing the length of the read) + List cigars = new ArrayList<>(); + for (int i = 0; i < 3; i++) { + CigarUnit u = CigarUnit.newBuilder().setOperationLength(2L).setOperation(ops1[i]).build(); + CigarUnit.newBuilder().setOperation(CigarUnit.Operation.SKIP); + cigars.add(u); + } + Read read2ValidOps = Read.newBuilder() + .setAlignment(LinearAlignment.newBuilder() + .addAllCigar(cigars) + .setPosition(com.google.genomics.v1.Position.newBuilder() + .setPosition(3L) + .setReferenceName("chr1")) + .setMappingQuality(15)) + .setReadGroupSetId("123").build(); + // Read 2 (Contains three operations that result in increasing the length of the read) + cigars.clear(); + for (int i = 0; i < 3; i++) { + CigarUnit u = CigarUnit.newBuilder().setOperationLength(1L).setOperation(ops2[i]).build(); + cigars.add(u); + } + Read read3ValidOps = Read.newBuilder() + .setAlignment(LinearAlignment.newBuilder() + .addAllCigar(cigars) + .setPosition(com.google.genomics.v1.Position.newBuilder() + .setPosition(2L) + .setReferenceName("chr1")) + .setMappingQuality(1)) + .setReadGroupSetId("123").build(); + // Read 3 (Unmapped) + Read unmappedRead = Read.newBuilder().build(); + // Read 4 (Contains one operation that results in increasing the length of the read) + cigars.clear(); + for (int i = 0; i < 3; i++) { + CigarUnit u = CigarUnit.newBuilder().setOperationLength(4L).setOperation(ops3[i]).build(); + cigars.add(u); + } + Read read1ValidOp = Read.newBuilder() + .setAlignment(LinearAlignment.newBuilder() + .addAllCigar(cigars) + .setPosition(com.google.genomics.v1.Position.newBuilder() + .setPosition(4L) + .setReferenceName("chr1")) + .setMappingQuality(1)) + .setReadGroupSetId("321").build(); + testSet = Lists.newArrayList(read2ValidOps, read3ValidOps, unmappedRead, read1ValidOp); + // Test data for testCalculateQuantiles + testSet2 = Lists.newArrayList(); + Position p = new Position().setPosition(1L).setReferenceName("chr1"); + testSet2.add(KV.of(new PosRgsMq(p, "123", PosRgsMq.MappingQuality.L), 4.0)); + testSet2.add(KV.of(new PosRgsMq(p, "123", PosRgsMq.MappingQuality.M), 2.0)); + testSet2.add(KV.of(new PosRgsMq(p, "123", PosRgsMq.MappingQuality.H), 0.5)); + testSet2.add(KV.of(new PosRgsMq(p, "123", PosRgsMq.MappingQuality.A), 6.5)); + testSet2.add(KV.of(new PosRgsMq(p, "321", PosRgsMq.MappingQuality.L), 5.0)); + testSet2.add(KV.of(new PosRgsMq(p, "321", PosRgsMq.MappingQuality.M), 1.0)); + testSet2.add(KV.of(new PosRgsMq(p, "321", PosRgsMq.MappingQuality.H), 0.75)); + testSet2.add(KV.of(new PosRgsMq(p, "321", PosRgsMq.MappingQuality.A), 6.75)); + testSet2.add(KV.of(new PosRgsMq(p, "456", PosRgsMq.MappingQuality.L), 4.6)); + testSet2.add(KV.of(new PosRgsMq(p, "456", PosRgsMq.MappingQuality.M), 3.2)); + testSet2.add(KV.of(new PosRgsMq(p, "456", PosRgsMq.MappingQuality.H), 1.2)); + testSet2.add(KV.of(new PosRgsMq(p, "456", PosRgsMq.MappingQuality.A), 9.0)); + testSet2.add(KV.of(new PosRgsMq(p, "654", PosRgsMq.MappingQuality.L), 3.0)); + testSet2.add(KV.of(new PosRgsMq(p, "654", PosRgsMq.MappingQuality.A), 3.0)); + testSet2.add(KV.of(new PosRgsMq(p, "789", PosRgsMq.MappingQuality.L), 8.0)); + testSet2.add(KV.of(new PosRgsMq(p, "789", PosRgsMq.MappingQuality.A), 8.0)); + // Test data for testCalculateCoverage + input = Lists.newArrayList(); + cigars.clear(); + for (int i = 0; i < 25; i++) { + cigars = new ArrayList<>(); + for (int j = 0; j < readLengthInfo[i]; j++) { + CigarUnit u = CigarUnit.newBuilder().setOperationLength(1L).setOperation(Operation.ALIGNMENT_MATCH).build(); + cigars.add(u); + } + Read read = Read.newBuilder() + .setAlignment(LinearAlignment.newBuilder() + .addAllCigar(cigars) + .setPosition(com.google.genomics.v1.Position.newBuilder() + .setPosition(readPosInfo[i]) + .setReferenceName("1")) + .setMappingQuality(readMQInfo[i])) + .setReadGroupSetId("Rgs" + i / 5 + 1).build(); + input.add(read); + } + } + + /** + * Unit test for CalculateCoverageMean composite PTransform + */ + @Test + public void testCalculateCoverageMean() { + // Expected Output + KV[] expectedOutput = new KV[12]; + PosRgsMq pTest = new PosRgsMq(new Position() + .setPosition(2L).setReferenceName("chr1"), "123", PosRgsMq.MappingQuality.L); + expectedOutput[0] = KV.of(pTest, 1.0); + pTest = new PosRgsMq(new Position() + .setPosition(2L).setReferenceName("chr1"), "123", PosRgsMq.MappingQuality.M); + expectedOutput[1] = KV.of(pTest, 0.5); + pTest = new PosRgsMq(new Position() + .setPosition(2L).setReferenceName("chr1"), "123", PosRgsMq.MappingQuality.A); + expectedOutput[2] = KV.of(pTest, 1.5); + pTest = new PosRgsMq(new Position() + .setPosition(4L).setReferenceName("chr1"), "123", PosRgsMq.MappingQuality.L); + expectedOutput[3] = KV.of(pTest, 0.5); + pTest = new PosRgsMq(new Position() + .setPosition(4L).setReferenceName("chr1"), "123", PosRgsMq.MappingQuality.M); + expectedOutput[4] = KV.of(pTest, 1.0); + pTest = new PosRgsMq(new Position() + .setPosition(4L).setReferenceName("chr1"), "123", PosRgsMq.MappingQuality.A); + expectedOutput[5] = KV.of(pTest, 1.5); + pTest = new PosRgsMq(new Position() + .setPosition(6L).setReferenceName("chr1"), "123", PosRgsMq.MappingQuality.M); + expectedOutput[6] = KV.of(pTest, 0.5); + pTest = new PosRgsMq(new Position() + .setPosition(6L).setReferenceName("chr1"), "123", PosRgsMq.MappingQuality.A); + expectedOutput[7] = KV.of(pTest, 0.5); + pTest = new PosRgsMq(new Position() + .setPosition(4L).setReferenceName("chr1"), "321", PosRgsMq.MappingQuality.L); + expectedOutput[8] = KV.of(pTest, 1.0); + pTest = new PosRgsMq(new Position() + .setPosition(4L).setReferenceName("chr1"), "321", PosRgsMq.MappingQuality.A); + expectedOutput[9] = KV.of(pTest, 1.0); + pTest = new PosRgsMq(new Position() + .setPosition(6L).setReferenceName("chr1"), "321", PosRgsMq.MappingQuality.L); + expectedOutput[10] = KV.of(pTest, 1.0); + pTest = new PosRgsMq(new Position() + .setPosition(6L).setReferenceName("chr1"), "321", PosRgsMq.MappingQuality.A); + expectedOutput[11] = KV.of(pTest, 1.0); + Pipeline p = TestPipeline.create(); + p.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + PCollection inputReads = p.apply(Create.of(testSet)); + PCollection> output = inputReads.apply(new CalculateCoverageMean()); + DataflowAssert.that(output).containsInAnyOrder(expectedOutput); + } + + /** + * Unit test for CalculateQuantiles composite PTransform + */ + @Test + public void testCalculateQuantiles() { + Pipeline p = TestPipeline.create(); + p.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + PCollection> inputMappingQualities = p.apply(Create.of(testSet2)); + PCollection>>> output = inputMappingQualities.apply( + new CalculateQuantiles(3)); + Position pos = new Position().setPosition(1L).setReferenceName("chr1"); + List low = Lists.newArrayList(3.0, 4.6, 8.0); + List med = Lists.newArrayList(1.0, 2.0, 3.2); + List high = Lists.newArrayList(0.5, 0.75, 1.2); + List all = Lists.newArrayList(3.0, 6.75, 9.0); + DataflowAssert.that(output).containsInAnyOrder( + KV.of(pos, KV.of(PosRgsMq.MappingQuality.L, low)), + KV.of(pos, KV.of(PosRgsMq.MappingQuality.M, med)), + KV.of(pos, KV.of(PosRgsMq.MappingQuality.H, high)), + KV.of(pos, KV.of(PosRgsMq.MappingQuality.A, all))); + } + + /** + * Testing the CalculateCoverage pipeline. + */ + @Test + public void testCalculateCoverage() throws Exception { + List expectedOutput = Lists.newArrayList(); + Annotation a1 = new Annotation() + .setAnnotationSetId("123") + .setPosition(new RangePosition() + .setStart(0L) + .setEnd(2L) + .setReferenceName("1")) + .setType("GENERIC") + .setInfo(new HashMap>()); + a1.getInfo().put("L", Lists.newArrayList("1.0", "1.0", "3.5")); + a1.getInfo().put("M", Lists.newArrayList("1.5", "1.5", "2.0")); + a1.getInfo().put("H", Lists.newArrayList("0.5", "0.5", "0.5")); + a1.getInfo().put("A", Lists.newArrayList("2.5", "3.0", "3.5")); + expectedOutput.add(a1); + Annotation a2 = new Annotation() + .setAnnotationSetId("123") + .setPosition(new RangePosition() + .setStart(2L) + .setEnd(4L) + .setReferenceName("1")) + .setType("GENERIC") + .setInfo(new HashMap>()); + a2.getInfo().put("L", Lists.newArrayList("1.0", "1.0", "3.0")); + a2.getInfo().put("M", Lists.newArrayList("0.5", "1.5", "1.5")); + a2.getInfo().put("H", Lists.newArrayList("0.5", "1.0", "1.0")); + a2.getInfo().put("A", Lists.newArrayList("2.0", "3.0", "3.0")); + expectedOutput.add(a2); + CalculateCoverage.Options popts = PipelineOptionsFactory.create().as( + CalculateCoverage.Options.class); + popts.setBucketWidth(TEST_BUCKET_WIDTH); + popts.setNumQuantiles(TEST_NUM_QUANTILES); + Pipeline p = TestPipeline.create(popts); + p.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + + PCollection reads = p.apply(Create.of(input)); + PCollection> coverageMeans = reads.apply( + new CalculateCoverage.CalculateCoverageMean()); + + PCollection>>> quantiles + = coverageMeans.apply(new CalculateCoverage.CalculateQuantiles(popts.getNumQuantiles())); + + PCollection>>>> answer + = quantiles.apply(GroupByKey.>>create()); + + PCollection output = answer.apply( + ParDo.of(new CalculateCoverage.CreateAnnotations("123", null, false))); + + DataflowAssert.that(output).containsInAnyOrder(expectedOutput); + + p.run(); + + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/pipelines/CountReadsITCase.java b/src/test/java/com/google/cloud/genomics/dataflow/pipelines/CountReadsITCase.java new file mode 100644 index 0000000..c75d187 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/pipelines/CountReadsITCase.java @@ -0,0 +1,207 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import java.io.BufferedReader; + +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +/** + * This integration test will read and write to Cloud Storage, and call the Genomics API. + * + * The following environment variables are required: + * - a Google Cloud API key in GOOGLE_API_KEY, + * - a Google Cloud project name in TEST_PROJECT, + * - a Cloud Storage folder path in TEST_OUTPUT_GCS_FOLDER to store temporary test outputs, + * - a Cloud Storage folder path in TEST_STAGING_GCS_FOLDER to store temporary files, + * + * Cloud Storage folder paths should be of the form "gs://bucket/folder/" + * + * When doing e.g. mvn install, you can skip integration tests using: + * mvn install -DskipITs + * + * To run one test: + * mvn -Dit.test=CountReadsITCase#testLocal verify + * + * See also http://maven.apache.org/surefire/maven-failsafe-plugin/examples/single-test.html + */ +@RunWith(JUnit4.class) +public class CountReadsITCase { + + // This file shouldn't move. + static final String TEST_BAM_FNAME = "gs://genomics-public-data/ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/data/NA06985/alignment/NA06985.454.MOSAIK.SRP000033.2009_11.bam"; + // This is the Readgroupset ID of the same file, in ReadStore. It also shouldn't move. + static final String TEST_READGROUPSET = "CMvnhpKTFhDvp9zAvYj66AY"; + // The region where we're counting reads. + static final String TEST_CONTIG = "1:550000:560000"; + // How many reads are in that region. + static final long TEST_EXPECTED = 685; + // In this file there are no unmapped reads, so expecting the same number. + static final long TEST_EXPECTED_WITH_UNMAPPED = TEST_EXPECTED; + + // Same as the above variables, but for the NA12877_S1 dataset. + static final String NA12877_S1_BAM_FILENAME = "gs://genomics-public-data/platinum-genomes/bam/NA12877_S1.bam"; + static final String NA12877_S1_READGROUPSET = "CMvnhpKTFhD3he72j4KZuyc"; + static final String NA12877_S1_CONTIG = "chr17:41196311:41277499"; + static final long NA12877_S1_EXPECTED = 45081; + // How many reads are in that region if we take unmapped ones too + static final long NA12877_S1_EXPECTED_WITH_UNMAPPED = 45142; + + static IntegrationTestHelper helper; + + @BeforeClass + public static void setUpBeforeClass() { + helper = new IntegrationTestHelper(); + } + + private void testLocalBase(String outputFilename, String contig, String bamFilename, long expectedCount, + boolean includeUnmapped) throws Exception { + final String OUTPUT = helper.getTestOutputGcsFolder()+ outputFilename; + String[] ARGS = { + "--output=" + OUTPUT, + "--references=" + contig, + "--includeUnmapped=" + includeUnmapped, + "--BAMFilePath=" + bamFilename, + }; + try { + helper.touchOutput(OUTPUT); + + CountReads.main(ARGS); + + BufferedReader reader = helper.openOutput(OUTPUT); + long got = Long.parseLong(reader.readLine()); + + Assert.assertEquals(expectedCount, got); + } finally { + helper.deleteOutput(OUTPUT); + } + } + + /** + * CountReads running on the client's machine. + */ + @Test + public void testLocal() throws Exception { + testLocalBase("CountReadsITCase-testLocal-output.txt", + TEST_CONTIG, TEST_BAM_FNAME, TEST_EXPECTED, false); + } + + @Test + public void testLocalUnmapped() throws Exception { + testLocalBase("CountReadsITCase-testLocal-output.txt", + TEST_CONTIG, TEST_BAM_FNAME, TEST_EXPECTED_WITH_UNMAPPED, true); + } + + @Test + public void testLocalNA12877_S1() throws Exception { + testLocalBase("CountReadsITCase-testLocal-NA12877_S1-output.txt", + NA12877_S1_CONTIG, NA12877_S1_BAM_FILENAME, NA12877_S1_EXPECTED, false); + } + + @Test + public void testLocalNA12877_S1_UNMAPPED() throws Exception { + testLocalBase("CountReadsITCase-testLocal-NA12877_S1-output.txt", + NA12877_S1_CONTIG, NA12877_S1_BAM_FILENAME, + NA12877_S1_EXPECTED_WITH_UNMAPPED, true); + } + + private void testCloudBase(String outputFilename, String contig, String bamFilename, long expectedCount) throws Exception { + final String OUTPUT = helper.getTestOutputGcsFolder() + outputFilename; + String[] ARGS = { + "--project=" + helper.getTestProject(), + "--output=" + OUTPUT, + "--numWorkers=2", + "--runner=BlockingDataflowPipelineRunner", + "--stagingLocation=" + helper.getTestStagingGcsFolder(), + "--references=" + contig, + "--BAMFilePath=" + bamFilename + }; + try { + helper.touchOutput(OUTPUT); + + CountReads.main(ARGS); + + BufferedReader reader = helper.openOutput(OUTPUT); + long got = Long.parseLong(reader.readLine()); + + Assert.assertEquals(expectedCount, got); + } finally { + helper.deleteOutput(OUTPUT); + } + } + + /** + * CountReads running on Dataflow. + */ + @Test + public void testCloud() throws Exception { + testCloudBase("CountReadsITCase-testCloud-output.txt", + TEST_CONTIG, TEST_BAM_FNAME, TEST_EXPECTED); + } + + @Test + public void testCloudNA12877_S1() throws Exception { + testCloudBase("CountReadsITCase-testCloud-NA12877_S1-output.txt", + NA12877_S1_CONTIG, NA12877_S1_BAM_FILENAME, NA12877_S1_EXPECTED); + } + + public void testCloudWithAPIBase(String outputFilename, String contig, String readGroupSetId, long expectedCount) throws Exception { + final String OUTPUT = helper.getTestOutputGcsFolder() + outputFilename; + String[] ARGS = { + "--project=" + helper.getTestProject(), + "--output=" + OUTPUT, + "--numWorkers=2", + "--runner=BlockingDataflowPipelineRunner", + "--stagingLocation=" + helper.getTestStagingGcsFolder(), + "--references=" + contig, + "--readGroupSetId=" + readGroupSetId + }; + try { + helper.touchOutput(OUTPUT); + + CountReads.main(ARGS); + + BufferedReader reader = helper.openOutput(OUTPUT); + long got = Long.parseLong(reader.readLine()); + + Assert.assertEquals(expectedCount, got); + } finally { + helper.deleteOutput(OUTPUT); + } + } + + /** + * CountReads running on Dataflow with API input. + */ + @Test + public void testCloudWithAPI() throws Exception { + testCloudWithAPIBase("CountReadsITCase-testCloudWithAPI-output.txt", + TEST_CONTIG, TEST_READGROUPSET, TEST_EXPECTED); + } + + @Test + public void testCloudWithAPI_NA12877_S1() throws Exception { + testCloudWithAPIBase("CountReadsITCase-testCloudWithAPI-NA12877_S1-output.txt", + NA12877_S1_CONTIG, NA12877_S1_READGROUPSET, NA12877_S1_EXPECTED); + } + + + +} \ No newline at end of file diff --git a/src/test/java/com/google/cloud/genomics/dataflow/pipelines/IntegrationTestHelper.java b/src/test/java/com/google/cloud/genomics/dataflow/pipelines/IntegrationTestHelper.java new file mode 100644 index 0000000..92bfa62 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/pipelines/IntegrationTestHelper.java @@ -0,0 +1,128 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertTrue; +import htsjdk.samtools.SamReader; +import htsjdk.samtools.ValidationStringency; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.Writer; +import java.nio.channels.Channels; +import java.security.GeneralSecurityException; + +import com.google.api.services.storage.Storage; +import com.google.cloud.dataflow.sdk.options.GcsOptions; +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.dataflow.sdk.util.GcsUtil; +import com.google.cloud.dataflow.sdk.util.Transport; +import com.google.cloud.dataflow.sdk.util.gcsfs.GcsPath; +import com.google.cloud.genomics.dataflow.readers.bam.BAMIO; +import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; + +public class IntegrationTestHelper { + + // Test configuration constants + private final String TEST_PROJECT = System.getenv("TEST_PROJECT"); + private final String TEST_OUTPUT_GCS_FOLDER = System.getenv("TEST_OUTPUT_GCS_FOLDER"); + private final String TEST_STAGING_GCS_FOLDER = System.getenv("TEST_STAGING_GCS_FOLDER"); + + // Variant test configuration constants + public static final String PLATINUM_GENOMES_DATASET = "3049512673186936334"; + public static final String PLATINUM_GENOMES_BRCA1_REFERENCES = "chr17:41196311:41277499"; + public static final int PLATINUM_GENOMES_NUMBER_OF_SAMPLES = 17; + + private GenomicsOptions popts = PipelineOptionsFactory.create().as(GenomicsOptions.class); + GcsUtil gcsUtil; + + public IntegrationTestHelper() { + assertNotNull("You must set the TEST_PROJECT environment variable for this test.", TEST_PROJECT); + assertNotNull("You must set the TEST_OUTPUT_GCS_FOLDER environment variable for this test.", TEST_OUTPUT_GCS_FOLDER); + assertNotNull("You must set the TEST_STAGING_GCS_FOLDER environment variable for this test.", TEST_STAGING_GCS_FOLDER); + assertTrue("TEST_OUTPUT_GCS_FOLDER must end with '/'", TEST_OUTPUT_GCS_FOLDER.endsWith("/")); + assertTrue("TEST_OUTPUT_GCS_FOLDER must start with 'gs://'", TEST_OUTPUT_GCS_FOLDER.startsWith("gs://")); + assertTrue("TEST_STAGING_GCS_FOLDER must start with 'gs://'", TEST_STAGING_GCS_FOLDER.startsWith("gs://")); + // we don't care how TEST_STAGING_GCS_FOLDER ends, so no check for it. + + gcsUtil = new GcsUtil.GcsUtilFactory().create(popts); + } + + /** + * @return the TEST_PROJECT + */ + public String getTestProject() { + return TEST_PROJECT; + } + + /** + * @return the TEST_OUTPUT_GCS_FOLDER + */ + public String getTestOutputGcsFolder() { + return TEST_OUTPUT_GCS_FOLDER; + } + + /** + * @return the TEST_STAGING_GCS_FOLDER + */ + public String getTestStagingGcsFolder() { + return TEST_STAGING_GCS_FOLDER; + } + + /** + * Make sure we can get to the output. + * + * Also write a sentinel value to the file. This protects against the possibility of prior + * test output causing a newly failing test to appear to succeed. + */ + public void touchOutput(String outputPath) throws IOException { + try (Writer writer = Channels.newWriter(gcsUtil.create(GcsPath.fromUri(outputPath), "text/plain"), "UTF-8")) { + writer.write("output will go here"); + } + } + + /** + * Open test output for reading. + */ + public BufferedReader openOutput(String outputPath) throws IOException { + return new BufferedReader(Channels.newReader(gcsUtil.open(GcsPath.fromUri(outputPath)), "UTF-8")); + } + + /** + * Open test output as BAM file - useful if your test writes out a BAM file + * and you want to validate the contents. + * @throws IOException + */ + public SamReader openBAM(String bamFilePath) throws IOException { + final GcsOptions gcsOptions = popts.as(GcsOptions.class); + final Storage.Objects storage = Transport.newStorageClient(gcsOptions).build().objects(); + return BAMIO.openBAM(storage, bamFilePath, ValidationStringency.LENIENT, true); + } + + /** + * Delete test output. + */ + public void deleteOutput(String outputPath) throws IOException, GeneralSecurityException { + // boilerplate + GcsPath path = GcsPath.fromUri(outputPath); + GcsOptions gcsOptions = (GcsOptions)popts.as(GcsOptions.class); + Storage storage = Transport.newStorageClient(gcsOptions).build(); + // do the actual work + storage.objects().delete(path.getBucket(), path.getObject()).execute(); + } + +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWritingITCase.java b/src/test/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWritingITCase.java new file mode 100644 index 0000000..c7d4f6d --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWritingITCase.java @@ -0,0 +1,97 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import htsjdk.samtools.BAMIndexMetaData; +import htsjdk.samtools.SamReader; + +/** + * This integration test will read and write to Cloud Storage, and call the Genomics API. + * + * The following environment variables are required: + * - a Google Cloud API key in GOOGLE_API_KEY, + * - a Google Cloud project name in TEST_PROJECT, + * - a Cloud Storage folder path in TEST_OUTPUT_GCS_FOLDER to store temporary test outputs, + * - a Cloud Storage folder path in TEST_STAGING_GCS_FOLDER to store temporary files, + * + * Cloud Storage folder paths should be of the form "gs://bucket/folder/" + * + * When doing e.g. mvn install, you can skip integration tests using: + * mvn install -DskipITs + * + * To run one test: + * mvn -Dit.test=ShardedBAMWritingITCase#testShardedWriting verify + * + * See also http://maven.apache.org/surefire/maven-failsafe-plugin/examples/single-test.html + */ +@RunWith(JUnit4.class) +public class ShardedBAMWritingITCase { + static final String TEST_CONTIG = "11:1:200000000"; + static final String TEST_BAM_FNAME = "gs://genomics-public-data/ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/NA12878/exome_alignment/NA12878.chrom11.ILLUMINA.bwa.CEU.exome.20121211.bam"; + static final String OUTPUT_FNAME = "sharded-output.bam"; + static final int EXPECTED_ALL_READS = 10414236; + static final int EXPECTED_UNMAPPED_READS = 108950; + + + static IntegrationTestHelper helper; + + @BeforeClass + public static void setUpBeforeClass() { + helper = new IntegrationTestHelper(); + } + + @Test + public void testShardedWriting() throws Exception { + final String OUTPUT = helper.getTestOutputGcsFolder() + OUTPUT_FNAME; + String[] ARGS = { + "--project=" + helper.getTestProject(), + "--output=" + OUTPUT, + "--numWorkers=18", + "--runner=BlockingDataflowPipelineRunner", + "--stagingLocation=" + helper.getTestStagingGcsFolder(), + "--references=" + TEST_CONTIG, + "--BAMFilePath=" + TEST_BAM_FNAME, + "--lociPerWritingShard=1000000" + }; + SamReader reader = null; + try { + helper.touchOutput(OUTPUT); + + ShardedBAMWriting.main(ARGS); + + reader = helper.openBAM(OUTPUT); + Assert.assertTrue(reader.hasIndex()); + final int sequenceIndex = reader.getFileHeader().getSequenceIndex("11"); + BAMIndexMetaData metaData = reader.indexing().getIndex().getMetaData(sequenceIndex); + Assert.assertEquals(EXPECTED_ALL_READS - EXPECTED_UNMAPPED_READS, + metaData.getAlignedRecordCount()); + Assert.assertEquals(EXPECTED_UNMAPPED_READS, + metaData.getUnalignedRecordCount()); + + } finally { + if (reader != null) { + reader.close(); + } + helper.deleteOutput(OUTPUT); + } + } +} \ No newline at end of file diff --git a/src/test/java/com/google/cloud/genomics/dataflow/pipelines/VariantSimilarityITCase.java b/src/test/java/com/google/cloud/genomics/dataflow/pipelines/VariantSimilarityITCase.java new file mode 100644 index 0000000..b5faaa1 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/pipelines/VariantSimilarityITCase.java @@ -0,0 +1,163 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.junit.Assert.assertEquals; + +import java.io.BufferedReader; +import java.io.IOException; +import java.security.GeneralSecurityException; +import java.util.List; + +import org.hamcrest.CoreMatchers; +import org.junit.After; +import org.junit.BeforeClass; +import org.junit.Test; + +import com.google.api.client.util.Lists; +import com.google.cloud.dataflow.sdk.util.gcsfs.GcsPath; +import com.google.cloud.genomics.dataflow.functions.PCoAnalysis.GraphResult; + +/** + * This integration test will call the Genomics API and write to Cloud Storage. + * + * The following environment variables are required: + * - a Google Cloud API key in GOOGLE_API_KEY, + * - a Google Cloud project name in TEST_PROJECT, + * - a Cloud Storage folder path in TEST_OUTPUT_GCS_FOLDER to store temporary test outputs, + * - a Cloud Storage folder path in TEST_STAGING_GCS_FOLDER to store temporary files, + * + * Cloud Storage folder paths should be of the form "gs://bucket/folder/" + * + * When doing e.g. mvn install, you can skip integration tests using: + * mvn install -DskipITs + * + * To run one test: + * mvn -Dit.test=VariantSimilarityITCase#testLocal verify + * + * See also http://maven.apache.org/surefire/maven-failsafe-plugin/examples/single-test.html + */ +public class VariantSimilarityITCase { + + static final GraphResult[] EXPECTED_RESULT = { + new GraphResult("NA12877", 5.18, 0.22), + new GraphResult("NA12878", -7.39, -1.7), + new GraphResult("NA12879", 5.26, 1.37), + new GraphResult("NA12880", -7.41, -2.74), + new GraphResult("NA12881", 5.27, -1.06), + new GraphResult("NA12882", 5.21, 1.19), + new GraphResult("NA12883", -7.57, -3.73), + new GraphResult("NA12884", 5.33, 0.95), + new GraphResult("NA12885", 5.21, 1.07), + new GraphResult("NA12886", 5.28, -0.15), + new GraphResult("NA12887", -7.44, 1.69), + new GraphResult("NA12888", -7.47, 2.72), + new GraphResult("NA12889", -7.34, 1.65), + new GraphResult("NA12890", 5.04, -1.61), + new GraphResult("NA12891", 5.24, -0.88), + new GraphResult("NA12892", -7.64, 2.1), + new GraphResult("NA12893", 5.18, -1.18) + }; + + static String outputPrefix; + static IntegrationTestHelper helper; + + @BeforeClass + public static void setUpBeforeClass() throws Exception { + helper = new IntegrationTestHelper(); + outputPrefix = helper.getTestOutputGcsFolder() + "variantSimilarity"; + } + + @After + public void tearDown() throws Exception { + for (GcsPath path : helper.gcsUtil.expand(GcsPath.fromUri(outputPrefix + "*"))) { + helper.deleteOutput(path.toString()); + } + } + + @Test + public void testPaginatedLocal() throws IOException, GeneralSecurityException { + String[] ARGS = { + "--references=" + helper.PLATINUM_GENOMES_BRCA1_REFERENCES, + "--variantSetId=" + helper.PLATINUM_GENOMES_DATASET, + "--output=" + outputPrefix, + "--useGrpc=false" + }; + testBase(ARGS); + } + + @Test + public void testPaginatedCloud() throws IOException, GeneralSecurityException { + String[] ARGS = { + "--references=" + helper.PLATINUM_GENOMES_BRCA1_REFERENCES, + "--variantSetId=" + helper.PLATINUM_GENOMES_DATASET, + "--output=" + outputPrefix, + "--project=" + helper.getTestProject(), + "--runner=BlockingDataflowPipelineRunner", + "--stagingLocation=" + helper.getTestStagingGcsFolder(), + "--useGrpc=false" + }; + testBase(ARGS); + } + + @Test + public void testStreamingLocal() throws IOException, GeneralSecurityException { + String[] ARGS = { + "--references=" + helper.PLATINUM_GENOMES_BRCA1_REFERENCES, + "--variantSetId=" + helper.PLATINUM_GENOMES_DATASET, + "--output=" + outputPrefix, + "--useGrpc=true" + }; + testBase(ARGS); + } + + @Test + public void testStreamingCloud() throws IOException, GeneralSecurityException { + String[] ARGS = { + "--references=" + helper.PLATINUM_GENOMES_BRCA1_REFERENCES, + "--variantSetId=" + helper.PLATINUM_GENOMES_DATASET, + "--output=" + outputPrefix, + "--project=" + helper.getTestProject(), + "--runner=BlockingDataflowPipelineRunner", + "--stagingLocation=" + helper.getTestStagingGcsFolder(), + "--useGrpc=true" + }; + testBase(ARGS); + } + + private void testBase(String[] ARGS) throws IOException, GeneralSecurityException { + // Run the pipeline. + VariantSimilarity.main(ARGS); + + // Download the pipeline results. + List results = Lists.newArrayList(); + for (GcsPath path : helper.gcsUtil.expand(GcsPath.fromUri(outputPrefix + "*"))) { + BufferedReader reader = helper.openOutput(path.toString()); + for (String line = reader.readLine(); line != null; line = reader.readLine()) { + results.add(GraphResult.fromString(line)); + } + } + + // Check the pipeline results. + assertEquals(helper.PLATINUM_GENOMES_NUMBER_OF_SAMPLES, results.size()); + + assertThat(results, + CoreMatchers.allOf(CoreMatchers.hasItems(EXPECTED_RESULT))); + } +} + + diff --git a/src/test/java/com/google/cloud/genomics/dataflow/pipelines/VerifyBamIdTest.java b/src/test/java/com/google/cloud/genomics/dataflow/pipelines/VerifyBamIdTest.java new file mode 100644 index 0000000..22b6fec --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/pipelines/VerifyBamIdTest.java @@ -0,0 +1,341 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.pipelines; + +import com.google.cloud.dataflow.sdk.Pipeline; +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.dataflow.sdk.testing.DataflowAssert; +import com.google.cloud.dataflow.sdk.testing.TestPipeline; +import com.google.cloud.dataflow.sdk.transforms.Create; +import com.google.cloud.dataflow.sdk.transforms.DoFnTester; +import com.google.cloud.dataflow.sdk.transforms.ParDo; +import com.google.cloud.dataflow.sdk.transforms.join.CoGbkResult; +import com.google.cloud.dataflow.sdk.transforms.join.CoGroupByKey; +import com.google.cloud.dataflow.sdk.transforms.join.KeyedPCollectionTuple; +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.cloud.dataflow.sdk.values.PCollection; +import com.google.cloud.dataflow.sdk.values.TupleTag; +import com.google.cloud.genomics.dataflow.coders.GenericJsonCoder; +import com.google.cloud.genomics.dataflow.model.AlleleFreq; +import com.google.cloud.genomics.dataflow.model.ReadBaseQuality; +import com.google.cloud.genomics.dataflow.model.ReadCounts; +import com.google.cloud.genomics.dataflow.model.ReadQualityCount; +import com.google.cloud.genomics.dataflow.pipelines.VerifyBamId.FilterFreq; +import com.google.cloud.genomics.dataflow.pipelines.VerifyBamId.GetAlleleFreq; +import com.google.cloud.genomics.dataflow.pipelines.VerifyBamId.PileupAndJoinReads; +import com.google.cloud.genomics.dataflow.pipelines.VerifyBamId.SampleReads; +import com.google.cloud.genomics.dataflow.pipelines.VerifyBamId.SplitReads; +import com.google.common.collect.ImmutableList; +import com.google.genomics.v1.CigarUnit; +import com.google.genomics.v1.CigarUnit.Operation; +import com.google.genomics.v1.LinearAlignment; +import com.google.genomics.v1.Position; +import com.google.genomics.v1.Read; +import com.google.genomics.v1.Variant; +import com.google.protobuf.ListValue; +import com.google.protobuf.Value; +import com.beust.jcommander.internal.Lists; + +import org.hamcrest.CoreMatchers; +import org.junit.Assert; +import org.junit.Test; + +/** + * Tests for the VerifyBamId pipeline. + */ +public class VerifyBamIdTest { + + @Test + public void testSplitReads() { + DoFnTester> splitReads = DoFnTester.of(new SplitReads()); + + // single matched base -> one SingleReadQuality proto + Read r = Read.newBuilder() + .setProperPlacement(true) + .setAlignment(LinearAlignment.newBuilder() + .setPosition(com.google.genomics.v1.Position.newBuilder() + .setReferenceName("1") + .setPosition(123)) + .addCigar(CigarUnit.newBuilder() + .setOperation(Operation.ALIGNMENT_MATCH) + .setOperationLength(1))) + .setAlignedSequence("A") + .addAlignedQuality(3) + .build(); + Assert.assertThat(splitReads.processBatch(r), CoreMatchers.hasItems(KV.of(Position.newBuilder() + .setReferenceName("1") + .setPosition(123L) + .build(), + new ReadBaseQuality("A", 3)))); + + // two matched bases -> two SingleReadQuality protos + r = Read.newBuilder() + .setProperPlacement(true) + .setAlignment(LinearAlignment.newBuilder() + .setPosition(com.google.genomics.v1.Position.newBuilder() + .setReferenceName("1") + .setPosition(123)) + .addCigar(CigarUnit.newBuilder() + .setOperation(Operation.ALIGNMENT_MATCH) + .setOperationLength(2))) + .setAlignedSequence("AG") + .addAllAlignedQuality(ImmutableList.of(3, 4)) + .build(); + Assert.assertThat(splitReads.processBatch(r), CoreMatchers.hasItems(KV.of(Position.newBuilder() + .setReferenceName("1") + .setPosition(123L) + .build(), + new ReadBaseQuality("A", 3)), + KV.of(Position.newBuilder() + .setReferenceName("1") + .setPosition(124L) + .build(), + new ReadBaseQuality("G", 4)))); + + // matched bases with different offsets onto the reference + r = Read.newBuilder() + .setProperPlacement(true) + .setAlignment(LinearAlignment.newBuilder() + .setPosition(com.google.genomics.v1.Position.newBuilder() + .setReferenceName("1") + .setPosition(123)) + .addCigar(CigarUnit.newBuilder() + .setOperation(Operation.INSERT) + .setOperationLength(1)) + .addCigar(CigarUnit.newBuilder() + .setOperation(Operation.ALIGNMENT_MATCH) + .setOperationLength(1)) + .addCigar(CigarUnit.newBuilder() + .setOperation(Operation.DELETE) + .setOperationLength(1)) + .addCigar(CigarUnit.newBuilder() + .setOperation(Operation.ALIGNMENT_MATCH) + .setOperationLength(2))) + // 1I1M1D2M; C -> ref 0, GT -> ref 2, 3 + .setAlignedSequence("ACGT") + .addAllAlignedQuality(ImmutableList.of(1, 2, 3, 4)) + .build(); + Assert.assertThat(splitReads.processBatch(r), CoreMatchers.hasItems(KV.of(Position.newBuilder() + .setReferenceName("1") + .setPosition(123L) + .build(), + new ReadBaseQuality("C", 2)), + KV.of(Position.newBuilder() + .setReferenceName("1") + .setPosition(125L) + .build(), + new ReadBaseQuality("G", 3)), + KV.of(Position.newBuilder() + .setReferenceName("1") + .setPosition(126L) + .build(), + new ReadBaseQuality("T", 4)))); + + // matched bases with different offsets onto the reference + r = Read.newBuilder() + .setAlignment(LinearAlignment.newBuilder() + .setPosition(com.google.genomics.v1.Position.newBuilder() + .setReferenceName("1") + .setPosition(123)) + .addCigar(CigarUnit.newBuilder() + .setOperation(Operation.DELETE) + .setOperationLength(1)) + .addCigar(CigarUnit.newBuilder() + .setOperation(Operation.ALIGNMENT_MATCH) + .setOperationLength(2)) + .addCigar(CigarUnit.newBuilder() + .setOperation(Operation.INSERT) + .setOperationLength(1)) + .addCigar(CigarUnit.newBuilder() + .setOperation(Operation.ALIGNMENT_MATCH) + .setOperationLength(1))) + // 1D2M1I1M; A and G match positions 1 and 3 of the ref + .setAlignedSequence("ACGT") + .addAllAlignedQuality(ImmutableList.of(1, 2, 3, 4)) + .build(); + Assert.assertThat(splitReads.processBatch(r), CoreMatchers.hasItems(KV.of(Position.newBuilder() + .setReferenceName("1") + .setPosition(124L) + .build(), + new ReadBaseQuality("A", 1)), + KV.of(Position.newBuilder() + .setReferenceName("1") + .setPosition(125L) + .build(), + new ReadBaseQuality("C", 2)), + KV.of(Position.newBuilder() + .setReferenceName("1") + .setPosition(126L) + .build(), + new ReadBaseQuality("T", 4)))); + } + + @Test + public void testSampleReads() { + SampleReads sampleReads = new SampleReads(0.5, ""); + Assert.assertTrue(sampleReads.apply(KV.of( + Position.newBuilder() + .setReferenceName("1") + .setPosition(125L) + .setReverseStrand(false) + .build(), + new ReadBaseQuality()))); + Assert.assertFalse(sampleReads.apply(KV.of( + Position.newBuilder() + .setReferenceName("2") + .setPosition(124L) + .setReverseStrand(false) + .build(), + new ReadBaseQuality()))); + } + + @Test + public void testGetAlleleFreq() { + DoFnTester> getAlleleFreq = DoFnTester.of( + new GetAlleleFreq()); + Position pos = Position.newBuilder() + .setReferenceName("1") + .setPosition(123L) + .build(); + Variant.Builder vBuild = Variant.newBuilder() + .setReferenceName("1") + .setStart(123L) + .setReferenceBases("C") + .addAlternateBases("T"); + vBuild.getMutableInfo().put("AF", ListValue.newBuilder() + .addValues(Value.newBuilder().setNumberValue(0.25).build()).build()); + AlleleFreq af = new AlleleFreq(); + af.setAltBases(Lists.newArrayList("T")); + af.setRefBases("C"); + af.setRefFreq(0.25); + Assert.assertThat(getAlleleFreq.processBatch(vBuild.build()), + CoreMatchers.hasItems(KV.of(pos, af))); + } + + @Test + public void testFilterFreq() { + FilterFreq filterFreq = new FilterFreq(0.01); + Position pos = Position.newBuilder() + .setReferenceName("1") + .setPosition(123L) + .build(); + AlleleFreq af = new AlleleFreq(); + af.setRefFreq(0.9999); + Assert.assertFalse(filterFreq.apply(KV.of(pos, af))); + af.setRefFreq(0.9901); + Assert.assertFalse(filterFreq.apply(KV.of(pos, af))); + af.setRefFreq(0.9899); + Assert.assertTrue(filterFreq.apply(KV.of(pos, af))); + } + + private final Position position1 + = Position.newBuilder() + .setReferenceName("1") + .setPosition(123L) + .build(); + private final Position position2 + = Position.newBuilder() + .setReferenceName("1") + .setPosition(124L) + .build(); + private final Position position3 + = Position.newBuilder() + .setReferenceName("1") + .setPosition(125L) + .build(); + + private final ImmutableList> refCountList; + { + ImmutableList.Builder> refBuilder + = ImmutableList.builder(); + AlleleFreq af = new AlleleFreq(); + af.setRefBases("A"); + af.setAltBases(Lists.newArrayList("G")); + af.setRefFreq(0.8); + refBuilder.add(KV.of(position1, af)); + af = new AlleleFreq(); + af.setRefBases("C"); + af.setAltBases(Lists.newArrayList("T")); + af.setRefFreq(0.5); + refBuilder.add(KV.of(position2, af)); + af = new AlleleFreq(); + af.setRefBases("T"); + af.setAltBases(Lists.newArrayList("C")); + af.setRefFreq(0.6); + refBuilder.add(KV.of(position3, af)); + refCountList = refBuilder.build(); + } + + @Test + public void testPileupAndJoinReads() { + VerifyBamId.Options popts = + PipelineOptionsFactory.create().as(VerifyBamId.Options.class); + Pipeline p = TestPipeline.create(popts); + p.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + ReadBaseQuality srq = new ReadBaseQuality("A", 10); + PCollection> readCounts = p.apply( + Create.of(KV.of(position1, srq))); + PCollection> refFreq = p.apply(Create.of(refCountList)); + TupleTag readCountsTag = new TupleTag<>(); + TupleTag refFreqTag = new TupleTag<>(); + PCollection> joined = KeyedPCollectionTuple + .of(readCountsTag, readCounts) + .and(refFreqTag, refFreq) + .apply(CoGroupByKey.create()); + PCollection> result = joined.apply( + ParDo.of(new PileupAndJoinReads(readCountsTag, refFreqTag))); + ReadCounts rc = new ReadCounts(); + rc.setRefFreq(0.8); + rc.addReadQualityCount(ReadQualityCount.Base.REF, 10, 1); + DataflowAssert.that(result).containsInAnyOrder(KV.of(position1, rc)); + } + + @Test + public void testCombineReads() { + VerifyBamId.Options popts = + PipelineOptionsFactory.create().as(VerifyBamId.Options.class); + Pipeline p = TestPipeline.create(popts); + p.getCoderRegistry().setFallbackCoderProvider(GenericJsonCoder.PROVIDER); + PCollection> refCounts = p.apply(Create.of(this.refCountList)); + + PCollection reads = p.apply(Create.of(Read.newBuilder() + .setProperPlacement(true) + .setAlignment(LinearAlignment.newBuilder() + .setPosition(com.google.genomics.v1.Position.newBuilder() + .setReferenceName("1") + .setPosition(123)) + .addCigar(CigarUnit.newBuilder() + .setOperation(Operation.ALIGNMENT_MATCH) + .setOperationLength(3))) + .setAlignedSequence("ATG") + .addAllAlignedQuality(ImmutableList.of(3, 4, 5)) + .build())); + + PCollection> results = + VerifyBamId.combineReads(reads, 1.0, "", refCounts); + ReadCounts one = new ReadCounts(); + one.setRefFreq(0.8); + one.addReadQualityCount(ReadQualityCount.Base.REF, 3, 1L); + ReadCounts two = new ReadCounts(); + two.setRefFreq(0.5); + two.addReadQualityCount(ReadQualityCount.Base.NONREF, 4, 1L); + ReadCounts three = new ReadCounts(); + three.setRefFreq(0.6); + three.addReadQualityCount(ReadQualityCount.Base.OTHER, 5, 1L); + DataflowAssert.that(results) + .containsInAnyOrder(KV.of(position1, one), KV.of(position2, two), KV.of(position3, three)); + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/readers/bam/BAMIOITCase.java b/src/test/java/com/google/cloud/genomics/dataflow/readers/bam/BAMIOITCase.java new file mode 100644 index 0000000..87509d6 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/readers/bam/BAMIOITCase.java @@ -0,0 +1,61 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers.bam; + +import htsjdk.samtools.SAMRecordIterator; +import htsjdk.samtools.SamReader; +import htsjdk.samtools.ValidationStringency; + +import java.io.IOException; + +import org.junit.Assert; +import org.junit.Before; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import com.google.api.services.storage.Storage; +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.dataflow.sdk.util.Transport; +import com.google.cloud.genomics.dataflow.utils.GCSOptions; + +@RunWith(JUnit4.class) +public class BAMIOITCase { + final String API_KEY = System.getenv("GOOGLE_API_KEY"); + final String TEST_BAM_FNAME = "gs://genomics-public-data/ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/data/NA06985/alignment/NA06985.454.MOSAIK.SRP000033.2009_11.bam"; + final int EXPECTED_UNMAPPED_READS_COUNT = 685; + + @Before + public void voidEnsureEnvVar() { + Assert.assertNotNull("You must set the GOOGLE_API_KEY environment variable for this test.", API_KEY); + } + + @Test + public void openBAMTest() throws IOException { + GCSOptions popts = PipelineOptionsFactory.create().as(GCSOptions.class); + final Storage.Objects storageClient = Transport.newStorageClient(popts).build().objects(); + + SamReader samReader = BAMIO.openBAM(storageClient, TEST_BAM_FNAME, ValidationStringency.DEFAULT_STRINGENCY); + SAMRecordIterator iterator = samReader.query("1", 550000, 560000, false); + int readCount = 0; + while (iterator.hasNext()) { + iterator.next(); + readCount++; + } + Assert.assertEquals("Unexpected count of unmapped reads", + EXPECTED_UNMAPPED_READS_COUNT, readCount); + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/readers/bam/BAMShardTest.java b/src/test/java/com/google/cloud/genomics/dataflow/readers/bam/BAMShardTest.java new file mode 100644 index 0000000..a6cee0e --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/readers/bam/BAMShardTest.java @@ -0,0 +1,41 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers.bam; + +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; +import org.junit.Test; + +import htsjdk.samtools.BAMFileIndexImpl; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; + +import java.util.Collections; + +import htsjdk.samtools.Chunk; + +@RunWith(JUnit4.class) +public class BAMShardTest { + @Test + public void testShardGrowth() { + BAMShard shard = new BAMShard("f","chr20",1); + Chunk chunk = new Chunk(1,20); + shard.addBin(Collections.singletonList(chunk),10); + assertEquals(9, shard.sizeInLoci()); + assertEquals(19, shard.approximateSizeInBytes()); + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/readers/bam/ShardingPolicyTest.java b/src/test/java/com/google/cloud/genomics/dataflow/readers/bam/ShardingPolicyTest.java new file mode 100644 index 0000000..622ef51 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/readers/bam/ShardingPolicyTest.java @@ -0,0 +1,69 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.readers.bam; + +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; +import org.junit.Assert; +import org.junit.Test; + +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; + +import java.util.Collections; + +import htsjdk.samtools.Chunk; + +@RunWith(JUnit4.class) +public class ShardingPolicyTest { + @Test + public void testShardPolicyBytes() { + BAMShard shard = new BAMShard("f","chr20",1); + Chunk chunk = new Chunk(1,11L*1024L*1024L << 16); + shard.addBin(Collections.singletonList(chunk),90000); + Assert.assertTrue( + "Shard of size " + shard.approximateSizeInBytes() + + " is NOT big enough but it should be", + ShardingPolicy.BYTE_SIZE_POLICY.shardBigEnough(shard)); + + shard = new BAMShard("f","chr20",1); + chunk = new Chunk(1,1L*1024L*1024L << 16); + shard.addBin(Collections.singletonList(chunk),90000); + Assert.assertFalse( + "Shard of size " + shard.approximateSizeInBytes() + + " is big enough but it should NOT be", + ShardingPolicy.BYTE_SIZE_POLICY.shardBigEnough(shard)); + } + + @Test + public void testShardPolicyLoci() { + BAMShard shard = new BAMShard("f","chr20",1); + Chunk chunk = new Chunk(1,9*1024*1024); + shard.addBin(Collections.singletonList(chunk),110000); + Assert.assertTrue( + "Shard of size " + shard.sizeInLoci() + + " is NOT big enough but it should be", + ShardingPolicy.LOCI_SIZE_POLICY.shardBigEnough(shard)); + + shard = new BAMShard("f","chr20",1); + chunk = new Chunk(1,9*1024*1024); + shard.addBin(Collections.singletonList(chunk),90000); + Assert.assertFalse( + "Shard of size " + shard.sizeInLoci() + + " is big enough but it should NOT be", + ShardingPolicy.LOCI_SIZE_POLICY.shardBigEnough(shard)); + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/utils/AnnotationUtilsTest.java b/src/test/java/com/google/cloud/genomics/dataflow/utils/AnnotationUtilsTest.java new file mode 100644 index 0000000..ea07ca4 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/utils/AnnotationUtilsTest.java @@ -0,0 +1,147 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNull; + +import com.google.api.services.genomics.model.Annotation; +import com.google.api.services.genomics.model.Int32Value; +import com.google.api.services.genomics.model.RangePosition; +import com.google.api.services.genomics.model.Transcript; +import com.google.api.services.genomics.model.TranscriptCodingSequence; +import com.google.api.services.genomics.model.TranscriptExon; +import com.google.cloud.genomics.dataflow.utils.AnnotationUtils.VariantEffect; +import com.google.common.base.Strings; +import com.google.common.collect.ImmutableList; + +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import htsjdk.samtools.util.SequenceUtil; + +@RunWith(JUnit4.class) +public class AnnotationUtilsTest { + @Test + public void testDetermineVariantTranscriptEffect_simpleShort() { + Annotation transcript = new Annotation() + .setPosition(new RangePosition().setReferenceName("1").setStart(2L).setEnd(9L)) + .setTranscript(new Transcript() + .setCodingSequence(new TranscriptCodingSequence().setStart(2L).setEnd(9L)) + .setExons(ImmutableList.of( + new TranscriptExon().setStart(2L).setEnd(9L).setFrame(new Int32Value().setValue(0))))); + + assertEquals("GATTACA -> GCTTACA, codon is GAT -> GCT, AA is D -> A", + VariantEffect.NONSYNONYMOUS_SNP, + AnnotationUtils.determineVariantTranscriptEffect(3L, "C", transcript, "GATTACA")); + assertEquals("ATGTGAA -> ATGTGGA, codon is TGA -> TGG, AA is STOP -> W", + VariantEffect.STOP_LOSS, + AnnotationUtils.determineVariantTranscriptEffect(7L, "G", transcript, "ATGTGAA")); + assertEquals("CCCAAAT -> CCCTAAT, codon is AAA -> TAA, AA is K -> STOP", + VariantEffect.STOP_GAIN, + AnnotationUtils.determineVariantTranscriptEffect(5L, "T", transcript, "CCCAAAT")); + assertEquals("GATTACA -> GACTACA, codon is GAT -> GAC, AA is D -> D", + VariantEffect.SYNONYMOUS_SNP, + AnnotationUtils.determineVariantTranscriptEffect(4L, "C", transcript, "GATTACA")); + assertNull("variant does not intersect transcript", + AnnotationUtils.determineVariantTranscriptEffect(123L, "C", transcript, "GATTACA")); + } + + @Test + public void testDetermineVariantTranscriptEffect_reverseStrand() { + Annotation transcript = new Annotation() + .setPosition( + new RangePosition().setReferenceName("1").setStart(2L).setEnd(20L).setReverseStrand(true)) + .setTranscript(new Transcript() + .setCodingSequence(new TranscriptCodingSequence().setStart(3L).setEnd(18L)) + .setExons(ImmutableList.of( + new TranscriptExon().setStart(2L).setEnd(7L).setFrame(new Int32Value().setValue(2)), + new TranscriptExon().setStart(10L).setEnd(20L).setFrame(new Int32Value().setValue(1))) + )); + + String bases = SequenceUtil.reverseComplement( + // First exon [10, 20) + "AC" + // 5' UTR + "ATG" + "ACG" + "GT" + + // intron + "CCC" + + // Second exon [2, 7) + "G" + "TAG" + + "G"); // 3' UTR + assertEquals("ATG -> ACG (reverse complement), AA is M -> T", + VariantEffect.NONSYNONYMOUS_SNP, + AnnotationUtils.determineVariantTranscriptEffect(16L, "G", transcript, bases)); + assertEquals("TAG -> CAG (reverse complement), AA is STOP -> Q", + VariantEffect.STOP_LOSS, + AnnotationUtils.determineVariantTranscriptEffect(5L, "G", transcript, bases)); + assertNull("mutates intron", + AnnotationUtils.determineVariantTranscriptEffect(9L, "C", transcript, bases)); + assertNull("mutates 5' UTR", + AnnotationUtils.determineVariantTranscriptEffect(19L, "C", transcript, bases)); + } + + @Test + public void testDetermineVariantTranscriptEffect_noncoding() { + Annotation transcript = new Annotation() + .setPosition(new RangePosition().setReferenceName("1").setStart(2L).setEnd(9L)) + .setTranscript(new Transcript() + .setExons(ImmutableList.of(new TranscriptExon().setStart(2L).setEnd(9L)))); + + assertNull(AnnotationUtils.determineVariantTranscriptEffect(3L, "C", transcript, "GATTACA")); + assertNull(AnnotationUtils.determineVariantTranscriptEffect(11L, "C", transcript, "GATTACA")); + } + + @Test + public void testDetermineVariantTranscriptEffect_frameless() { + Annotation transcript = new Annotation() + .setPosition(new RangePosition().setReferenceName("1").setStart(2L).setEnd(9L)) + .setTranscript(new Transcript() + .setCodingSequence(new TranscriptCodingSequence().setStart(2L).setEnd(9L)) + .setExons(ImmutableList.of(new TranscriptExon().setStart(2L).setEnd(9L)))); + + assertNull(AnnotationUtils.determineVariantTranscriptEffect(3L, "C", transcript, "GATTACA")); + assertNull(AnnotationUtils.determineVariantTranscriptEffect(11L, "C", transcript, "GATTACA")); + } + + @Test + public void testDetermineVariantTranscriptEffect_multiExon() { + String bases = Strings.repeat("ACTTGGGTCA", 60); + Annotation transcript = new Annotation() + .setPosition(new RangePosition().setReferenceName("1").setStart(100L).setEnd(700L)) + .setTranscript(new Transcript() + .setCodingSequence(new TranscriptCodingSequence().setStart(250L).setEnd(580L)) + .setExons(ImmutableList.of( + new TranscriptExon().setStart(100L).setEnd(180L), + new TranscriptExon().setStart(200L).setEnd(300L).setFrame(new Int32Value().setValue(2)), + new TranscriptExon().setStart(400L).setEnd(500L).setFrame(new Int32Value().setValue(1)), + new TranscriptExon().setStart(550L).setEnd(600L).setFrame(new Int32Value().setValue(0))) + )); + + assertNull("mutates noncoding exon", + AnnotationUtils.determineVariantTranscriptEffect(150L, "C", transcript, bases)); + assertNull("mutates noncoding region of coding exon", + AnnotationUtils.determineVariantTranscriptEffect(240L, "C", transcript, bases)); + assertNull("mutates intron", + AnnotationUtils.determineVariantTranscriptEffect(350L, "C", transcript, bases)); + assertEquals("mutates first coding base, ACT -> TCT", + VariantEffect.NONSYNONYMOUS_SNP, + AnnotationUtils.determineVariantTranscriptEffect(250L, "T", transcript, bases)); + assertEquals("mutates middle exon, TGG -> TCG", + VariantEffect.NONSYNONYMOUS_SNP, + AnnotationUtils.determineVariantTranscriptEffect(454L, "C", transcript, bases)); + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/utils/DataUtils.java b/src/test/java/com/google/cloud/genomics/dataflow/utils/DataUtils.java new file mode 100644 index 0000000..ea8f3da --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/utils/DataUtils.java @@ -0,0 +1,52 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import java.util.Arrays; +import java.util.List; + +import com.google.api.services.genomics.model.Call; +import com.google.api.services.genomics.model.Variant; +import com.google.genomics.v1.VariantCall; +import com.google.genomics.v1.VariantCall.Builder; + +public class DataUtils { + + public static Call makeCall(String name, Integer... alleles) { + return new Call().setCallSetName(name).setGenotype(Arrays.asList(alleles)); + } + + public static VariantCall makeVariantCall(String name, Integer... alleles) { + return VariantCall.newBuilder() + .setCallSetName(name) + .addAllGenotype(Arrays.asList(alleles)) + .build(); + } + + public static Variant makeSimpleVariant(Call... calls) { + return new Variant().setCalls(Arrays.asList(calls)); + } + + public static Variant makeVariant(String referenceName, long start, long end, + String referenceBases, List alternateBases, Call... calls) { + Variant variant = + new Variant().setReferenceName(referenceName).setStart(start).setEnd(end) + .setReferenceBases(referenceBases).setAlternateBases(alternateBases); + if (null != calls) { + variant.setCalls(Arrays.asList(calls)); + } + return variant; + } + +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/utils/GCSHelperITCase.java b/src/test/java/com/google/cloud/genomics/dataflow/utils/GCSHelperITCase.java new file mode 100644 index 0000000..691d89e --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/utils/GCSHelperITCase.java @@ -0,0 +1,111 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + + +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.io.InputStream; +import java.security.DigestInputStream; +import java.security.MessageDigest; +import java.security.NoSuchAlgorithmException; +import java.util.Arrays; + +import org.junit.Assert; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; +import com.google.cloud.genomics.utils.OfflineAuth; + +/** + * + * This test expects you to have a Google Cloud API key in the GOOGLE_API_KEY environment variable. + * It will read from GCS, so it's not your usual unit test (hence the integration test-related name). + * + */ +@RunWith(JUnit4.class) +public class GCSHelperITCase { + + // this file shouldn't move. + final String TEST_BUCKET = "genomics-public-data"; + final String TEST_FNAME = "ftp-trace.ncbi.nih.gov/1000genomes/ftp/20131219.populations.tsv"; + final long TEST_FSIZE = 1663; + final byte[] TEST_MD5 = new byte[] {-6, 94, 5, 25, 38, 68, 74, -127, -13, 94, -72, 7, -53, 111, 99, -3}; + + // Test the various ways of getting a GCSHelper + + @Test + public void testOfflineAuth() throws Exception { + GenomicsOptions options = PipelineOptionsFactory.as(GenomicsOptions.class); + OfflineAuth offlineAuth = GenomicsOptions.Methods.getGenomicsAuth(options); + GCSHelper gcsHelper = new GCSHelper(offlineAuth); + long fileSize = gcsHelper.getFileSize(TEST_BUCKET, TEST_FNAME); + Assert.assertEquals(TEST_FSIZE, fileSize); + } + + @Test + public void testPipelineOptions() throws Exception { + GenomicsOptions options = PipelineOptionsFactory.as(GenomicsOptions.class); + GCSHelper gcsHelper = new GCSHelper(options); + long fileSize = gcsHelper.getFileSize(TEST_BUCKET, TEST_FNAME); + Assert.assertEquals(TEST_FSIZE, fileSize); + } + + // Test the GCSHelper's methods + + @Test + public void testGetPartial() throws Exception { + GenomicsOptions options = PipelineOptionsFactory.as(GenomicsOptions.class); + GCSHelper gcsHelper = new GCSHelper(options); + String partial = gcsHelper.getPartialObjectData(TEST_BUCKET, TEST_FNAME, 34, 37).toString(); + Assert.assertEquals("Code", partial); + } + + @Test + public void testGetWhole() throws Exception { + GenomicsOptions options = PipelineOptionsFactory.as(GenomicsOptions.class); + GCSHelper gcsHelper = new GCSHelper(options); + InputStream input = gcsHelper.getWholeObject(TEST_BUCKET, TEST_FNAME); + byte[] digest = md5sum(input); + Assert.assertTrue("file MD5 doesn't match.", Arrays.equals(TEST_MD5, digest)); + } + + @Test + public void testDownload() throws Exception { + GenomicsOptions options = PipelineOptionsFactory.as(GenomicsOptions.class); + GCSHelper gcsHelper = new GCSHelper(options); + File tmpFile = gcsHelper.getAsFile(TEST_BUCKET, TEST_FNAME); + byte[] digest = md5sum(new FileInputStream(tmpFile)); + Assert.assertTrue("file MD5 doesn't match.", Arrays.equals(TEST_MD5, digest)); + } + + + private byte[] md5sum(InputStream input) throws NoSuchAlgorithmException, IOException { + MessageDigest md = MessageDigest.getInstance("MD5"); + DigestInputStream dis = new DigestInputStream(input, md); + byte[] buf = new byte[1024*1024]; + while (true) { + int read = dis.read(buf); + // EOF + if (read<=0) break; + } + return md.digest(); + } + +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/utils/PairGeneratorTest.java b/src/test/java/com/google/cloud/genomics/dataflow/utils/PairGeneratorTest.java new file mode 100644 index 0000000..7250253 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/utils/PairGeneratorTest.java @@ -0,0 +1,51 @@ +/* + * Copyright (C) 2014 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not + * use this file except in compliance with the License. You may obtain a copy of + * the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT + * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the + * License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertThat; + +import org.hamcrest.CoreMatchers; +import org.junit.Test; + +import com.google.cloud.dataflow.sdk.values.KV; +import com.google.common.collect.FluentIterable; +import com.google.common.collect.ImmutableList; + +public class PairGeneratorTest { + + @Test + public void testAllPairsWithReplacement() { + FluentIterable> pairs = + PairGenerator.WITH_REPLACEMENT.allPairs(ImmutableList.of("one", "two", "three"), + String.CASE_INSENSITIVE_ORDER); + assertEquals(6, pairs.size()); + assertThat( + pairs, + CoreMatchers.hasItems(KV.of("one", "one"), KV.of("one", "two"), KV.of("one", "three"), + KV.of("two", "two"), KV.of("three", "two"), KV.of("three", "three"))); + } + + @Test + public void testAllPairsWithoutReplacement() { + FluentIterable> pairs = + PairGenerator.WITHOUT_REPLACEMENT.allPairs(ImmutableList.of("one", "two", "three"), + String.CASE_INSENSITIVE_ORDER); + assertEquals(3, pairs.size()); + assertThat(pairs, + CoreMatchers.hasItems(KV.of("one", "two"), KV.of("one", "three"), KV.of("three", "two"))); + } +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/utils/ReadFunctionsTest.java b/src/test/java/com/google/cloud/genomics/dataflow/utils/ReadFunctionsTest.java new file mode 100644 index 0000000..d1a67b7 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/utils/ReadFunctionsTest.java @@ -0,0 +1,368 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; + +import com.google.cloud.genomics.dataflow.model.ReadBaseQuality; +import com.google.cloud.genomics.dataflow.model.ReadBaseWithReference; +import com.google.common.collect.ImmutableList; +import com.google.common.collect.ImmutableMap; +import com.google.genomics.v1.CigarUnit; +import com.google.genomics.v1.CigarUnit.Operation; +import com.google.genomics.v1.LinearAlignment; +import com.google.genomics.v1.Position; +import com.google.genomics.v1.Read; + +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import java.io.IOException; +import java.util.List; +import java.util.Map; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +/** + * Tests for the ReadUtils class. + */ +@RunWith(JUnit4.class) +public class ReadFunctionsTest { + + /** + * Test whether a char is a valid base (ACGT) + */ + private static boolean isBase(char c) { + return c == 'A' || c == 'C' || c == 'G' || c == 'T'; + } + + static class CigarTestCase { + + /** + * All tests are on 'chr1' for now (it doesn't matter). + */ + private static final String CHROMOSOME = "1"; + + /** + * All read alignments start at position 10000 (it doesn't matter). + */ + private static final Integer INITIAL_OFFSET = 10000; + + /** + * String for a regular expression for a single CIGAR chunk. + */ + private static final String CIGAR_CHUNK = "[0-9]+[MIDNSHPX=]"; + + /** + * Regular expression for a single CIGAR chunk. + */ + private static final Pattern CIGAR_CHUNK_PATTERN = Pattern.compile(CIGAR_CHUNK); + + /** + * Convert from string to Operation. + */ + private static final Map CIGAR_UNIT_OPERATION + = new ImmutableMap.Builder() + .put("M", Operation.ALIGNMENT_MATCH) + .put("H", Operation.CLIP_HARD) + .put("S", Operation.CLIP_SOFT) + .put("D", Operation.DELETE) + .put("I", Operation.INSERT) + .put("P", Operation.PAD) + .put("=", Operation.SEQUENCE_MATCH) + .put("X", Operation.SEQUENCE_MISMATCH) + .put("N", Operation.SKIP) + .build(); + + final char[] alignedRef; + final char[] alignedSeq; + final String cigar; + final Read read; + final List readBases; + + /** + * Builds a test case containing a read that can be passed to the Cigar class and the expected + * read base results. + * + * @param seq The actual read sequence + * @param qualityScores The list of quality scores, one for each read base + * @param cigar The cigar string + * @param alignedRef The reference sequence adjusted to be aligned + * @param alignedSeq The read sequence adjusted to be aligned + * @param refSeqs One sequence for each piece of the cigar string, corresponding to the + * reference sequence for each piece + * @param refSeqStart Where on the reference sequence the read starts + */ + CigarTestCase(String seq, List qualityScores, String cigar, + String alignedRef, String alignedSeq, List refSeqs, + Integer refSeqStart) { + + if (alignedRef == null) { + this.alignedRef = null; + } else { + this.alignedRef = alignedRef.toCharArray(); + } + if (alignedSeq == null) { + this.alignedSeq = null; + } else { + this.alignedSeq = alignedSeq.toCharArray(); + } + + this.cigar = cigar; + this.read = Read.newBuilder() + .setAlignedSequence(seq) + .addAllAlignedQuality(qualityScores) + .setAlignment(LinearAlignment.newBuilder() + .setPosition(Position.newBuilder() + .setReferenceName(CHROMOSOME) + .setPosition(INITIAL_OFFSET + refSeqStart) + .build()) + .addAllCigar(cigarStringToUnits(cigar, refSeqs)) + .build()) + .build(); + this.readBases = buildReadBaseList(alignedSeq, alignedRef, qualityScores, + CHROMOSOME, INITIAL_OFFSET); + } + + /** + * Constructs the expected read base list for comparison with the results from the Cigar class. + * + * @param alignedSeq The read sequence adjusted to be aligned with the reference + * @param alignedRef The reference sequence adjusted to be aligned + * @param quals The quality score for each read base + * @param chromosome The chromosome where the alignment is + * @param originalPos The position of the first read base on the chromosome + * @return A constructed read base list + */ + private static List buildReadBaseList(String alignedSeq, + String alignedRef, List quals, + String chromosome, Integer originalPos) { + + if ((alignedSeq == null) || (alignedRef == null)) { + return null; + } + + if (alignedSeq.length() > alignedRef.length()) { + throw new IllegalArgumentException("The alignedRef is shorter than the alignedSeq:" + + alignedSeq.length() + " vs " + alignedRef.length()); + } + + int refPositionOffset = 0; + int qualityOffset = 0; + ImmutableList.Builder readBaseList = ImmutableList.builder(); + for (int i = 0; i < alignedSeq.length(); i++) { + // we only have a ReadBase if there is a base here in *BOTH* the reference + // and the read sequence. + if ((!isBase(alignedSeq.charAt(i))) + || (!isBase(alignedRef.charAt(i)))) { + // if the reference has a base but the sequence does not + if (alignedRef.charAt(i) != '*') { + refPositionOffset++; + } + if (isBase(Character.toUpperCase(Character.toUpperCase(alignedSeq.charAt(i))))) { + qualityOffset++; + } + continue; + } + + ReadBaseWithReference sr = new ReadBaseWithReference( + new ReadBaseQuality( + alignedSeq.substring(i, i + 1), + quals.get(qualityOffset)), + alignedRef.substring(i, i + 1), + Position.newBuilder() + .setReferenceName(chromosome) + .setPosition((long) (originalPos + refPositionOffset)) + .build()); + qualityOffset++; + refPositionOffset++; + readBaseList.add(sr); + } + + return readBaseList.build(); + } + + /** + * For testing, it's easier to set up the tests accurately using strings for the cigars. + * + * @param s cigar string to be converted into CigarUnits. + * @return list of CigarUnits. + */ + private static List cigarStringToUnits(String s, List refSeqs) { + + ImmutableList.Builder cigarUnits = ImmutableList.builder(); + + // check for an empty cigar string + if ("*".equals(s)) { + return cigarUnits.build(); + } + + // index into the list of reference sequences + int i = 0; + Matcher m = CIGAR_CHUNK_PATTERN.matcher(s); + while (m.find()) { + cigarUnits.add(CigarUnit.newBuilder() + .setOperation(CIGAR_UNIT_OPERATION.get(m.group().substring(m.group().length() - 1))) + .setOperationLength(Integer.parseInt(m.group().substring(0, m.group().length() - 1))) + .setReferenceSequence(!refSeqs.isEmpty() ? refSeqs.get(i) : "") + .build()); + i++; + } + + return cigarUnits.build(); + } + + } + + /* The test cases below are taken from the SAM file spec. + * For the quality scores, we use different increasing numbers to validate + * indexes into the quality list. + */ + static final List cases; + + static { + ImmutableList.Builder caseBuilder = ImmutableList.builder(); + // no cigar string + caseBuilder.add(new CigarTestCase( + "TTAGATAAAGGATACTG", + ImmutableList.of(10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, + 24, 25, 26), + "*", + null, + null, + null, + 0)); + + caseBuilder.add(new CigarTestCase( + "TTAGATAAAGGATACTG", + ImmutableList.of(10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, + 24, 25, 26), + "8M2I4M1D3M", + "AGCATGTTAGATAA**GATAGCTGTGCTAGTAGGCAGTCAGCGCCAT", + " TTAGATAAAGGATA*CTG", + ImmutableList.of("TTAGATAA", "**", "GATA", "", "CTG"), + 6)); + + caseBuilder.add(new CigarTestCase( + "AAAAGATAAGGATA", + ImmutableList.of(10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23), + "3S6M1P1I4M", + "AGCATGTTAGATAA**GATAGCTGTGCTAGTAGGCAGTCAGCGCCAT", + " aaaAGATAA*GGATA", + ImmutableList.of("", "AGATAA", "*", "*", "GATA"), + 8)); + + caseBuilder.add(new CigarTestCase( + "GCCTAAGCTAA", + ImmutableList.of(10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20), + "5S6M", + "AGCATGTTAGATAA**GATAGCTGTGCTAGTAGGCAGTCAGCGCCAT", + " gcctaAGCTAA", + ImmutableList.of("", "AGATAA"), + 8)); + + caseBuilder.add(new CigarTestCase( + "ATAGCTTCAGC", + ImmutableList.of(10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20), + "6M14N5M", + "AGCATGTTAGATAA**GATAGCTGTGCTAGTAGGCAGTCAGCGCCAT", + " ATAGCT..............TCAGC", + ImmutableList.of("ATAGCT", "GTGCTAGTAGGCAG", "TCAGC"), + 15)); + + caseBuilder.add(new CigarTestCase( + "TAGGC", + ImmutableList.of(10, 11, 12, 13, 14), + "6H5M", + "AGCATGTTAGATAA**GATAGCTGTGCTAGTAGGCAGTCAGCGCCAT", + // The spec has ttagctTAGGC instead of TAGGC. We're + // dropping the ttagct prefix because it's been + // pruned out before we get to toCigarOffset. + " TAGGC", + ImmutableList.of("", "TAGGC"), + 28)); + + caseBuilder.add(new CigarTestCase( + "CAGCGGCAT", + ImmutableList.of(10, 11, 12, 13, 14, 15, 16, 17, 18), + "9M", + "AGCATGTTAGATAA**GATAGCTGTGCTAGTAGGCAGTCAGCGCCAT", + " CAGCGGCAT", + ImmutableList.of("CAGCGCCAT"), + 36)); + + cases = caseBuilder.build(); + } + + @Test + public void testReadBases() throws IOException { + for (CigarTestCase tc : cases) { + assertEquals(tc.readBases, ReadFunctions.extractReadBases(tc.read)); + } + } + + @Test + public void testIsOnChromosome() { + assertFalse(ReadFunctions.IS_ON_CHROMOSOME.apply(Read.newBuilder() + .setAlignment(LinearAlignment.newBuilder() + .setPosition(Position.newBuilder() + .setReferenceName("chrZ") + .build()) + .build()) + .build())); + assertTrue(ReadFunctions.IS_ON_CHROMOSOME.apply(Read.newBuilder() + .setAlignment(LinearAlignment.newBuilder() + .setPosition(Position.newBuilder() + .setReferenceName("1") + .build()) + .build()) + .build())); + } + + @Test + public void testIsNotQCFailure() { + assertFalse(ReadFunctions.IS_NOT_QC_FAILURE.apply(Read.newBuilder() + .setFailedVendorQualityChecks(true) + .build())); + assertTrue(ReadFunctions.IS_NOT_QC_FAILURE.apply(Read.newBuilder() + .setFailedVendorQualityChecks(false) + .build())); + } + + @Test + public void testIsNotDuplicate() { + assertFalse(ReadFunctions.IS_NOT_DUPLICATE.apply(Read.newBuilder() + .setDuplicateFragment(true) + .build())); + assertTrue(ReadFunctions.IS_NOT_DUPLICATE.apply(Read.newBuilder() + .setDuplicateFragment(false) + .build())); + } + + @Test + public void testIsProperPlacement() { + assertTrue(ReadFunctions.IS_PROPER_PLACEMENT.apply(Read.newBuilder() + .setProperPlacement(true) + .build())); + assertFalse(ReadFunctions.IS_PROPER_PLACEMENT.apply(Read.newBuilder() + .setProperPlacement(false) + .build())); + } + +} diff --git a/src/test/java/com/google/cloud/genomics/dataflow/utils/SolverTest.java b/src/test/java/com/google/cloud/genomics/dataflow/utils/SolverTest.java new file mode 100644 index 0000000..0f2a6c0 --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/utils/SolverTest.java @@ -0,0 +1,174 @@ +/* + * Copyright 2015 Google. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import com.google.cloud.genomics.dataflow.functions.LikelihoodFn; +import com.google.cloud.genomics.dataflow.model.ReadCounts; +import com.google.cloud.genomics.dataflow.model.ReadQualityCount; +import com.google.cloud.genomics.dataflow.model.ReadQualityCount.Base; +import com.google.common.collect.ImmutableMap; +import com.google.genomics.v1.Position; + +import junit.framework.TestCase; + +import org.apache.commons.math3.analysis.UnivariateFunction; +import org.apache.commons.math3.geometry.euclidean.oned.Interval; +import org.apache.commons.math3.util.Precision; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import java.util.Map; + +/** + * Unit tests for Solver. + */ +@RunWith(JUnit4.class) +public class SolverTest extends TestCase { + + /** Parabola with maximum value at a specified point */ + public class Parabola implements UnivariateFunction { + private final double max; + + /** Create a Parabola with maximum at the specified value */ + Parabola(double max) { + this.max = max; + } + + @Override + public double value(double x) { + return 1.0 - Math.pow(x - this.max, 2.0); + } + } + + @Test + public void testGridSearch() { + Interval interval = Solver.gridSearch(new Parabola(0.25), 0.0, 1.0, 0.1); + assertEquals(Precision.compareTo(interval.getInf(), 0.1, 1), 0); + assertEquals(Precision.compareTo(interval.getSup(), 0.3, 1), 0); + + interval = Solver.gridSearch(new Parabola(1.2), 0.0, 1.0, 0.1); + assertEquals(Precision.compareTo(interval.getInf(), 0.9, 1), 0); + assertEquals(Precision.compareTo(interval.getSup(), 1.0, 1), 0); + + interval = Solver.gridSearch(new Parabola(1.2), 0.0, 1.0, 0.3); + assertEquals(Precision.compareTo(interval.getInf(), 0.9, 1), 0); + assertEquals(Precision.compareTo(interval.getSup(), 1.0, 1), 0); + } + + @Test + public void testMaximize() { + assertEquals(Precision.compareTo(Solver.maximize(new Parabola(0.47), 0.0, 1.0, + 0.1, 0.00001, 0.00001, 100, 100), 0.47, 0.00001), 0); + } + + @Test + public void testSolverOnKnownLikelihoodCases() { + int phred = 200; + + Position position1 = Position.newBuilder() + .setReferenceName("1") + .setPosition(123L) + .build(); + + /* + * Observe 900 REF reads and 100 NONREF + * P(REF) = 0.8 + * error probability is near 0 + * Most likely explanation should be ~20% contamination + * (if P(REF) were 0.5, we'd have peaks at 10% (nonref homozygous contaminant) + * and 20% (heterozygous contaminant) + */ + ImmutableMap.Builder countsBuilder + = ImmutableMap.builder(); + ReadCounts rc = new ReadCounts(); + rc.setRefFreq(0.8); + ReadQualityCount rqc = new ReadQualityCount(); + rqc.setBase(Base.REF); + rqc.setQuality(phred); + rqc.setCount(900); + rc.addReadQualityCount(rqc); + rqc = new ReadQualityCount(); + rqc.setBase(Base.NONREF); + rqc.setQuality(phred); + rqc.setCount(100); + rc.addReadQualityCount(rqc); + rqc = new ReadQualityCount(); + rqc.setBase(Base.OTHER); + rqc.setQuality(1); + rqc.setCount(2); + rc.addReadQualityCount(rqc); + countsBuilder.put(position1, rc); + Map readCounts = countsBuilder.build(); + assertEquals(Precision.compareTo(Solver.maximize( + new LikelihoodFn(readCounts), 0.0, 0.5, 0.05, + 0.0001, 0.0001, 100, 100), 0.2, 0.0001), 0); + + /* + * Make sure things are symmetrical. Observe 900 NONREF reads and 100 REF + * P(NONREF) = 0.8 (i.e. P(REF) = 0.2) + * error probability is near 0 + * Most likely explanation should be ~20% contamination + * (if P(REF) were 0.5, we'd have peaks at 10% (nonref homozygous contaminant) + * and 20% (heterozygous contaminant) + */ + countsBuilder = ImmutableMap.builder(); + rc = new ReadCounts(); + rc.setRefFreq(0.2); + rqc = new ReadQualityCount(); + rqc.setBase(Base.NONREF); + rqc.setQuality(phred); + rqc.setCount(900); + rc.addReadQualityCount(rqc); + rqc = new ReadQualityCount(); + rqc.setBase(Base.REF); + rqc.setQuality(phred); + rqc.setCount(100); + rc.addReadQualityCount(rqc); + countsBuilder.put(position1, rc); + readCounts = countsBuilder.build(); + assertEquals(Precision.compareTo(Solver.maximize( + new LikelihoodFn(readCounts), 0.0, 0.5, 0.05, + 0.0001, 0.0001, 100, 100), 0.2, 0.0001), 0); + + /* + * Assume a heterozygous desired base pair with a homozygous contaminant. + * Observe 450 NONREF reads and 550 REF + * P(REF) = 0.8 + * error probability is near 0 + * Most likely explanation should be ~10% contamination + */ + countsBuilder = ImmutableMap.builder(); + rc = new ReadCounts(); + rc.setRefFreq(0.5); + rqc = new ReadQualityCount(); + rqc.setBase(Base.NONREF); + rqc.setQuality(phred); + rqc.setCount(450); + rc.addReadQualityCount(rqc); + rqc = new ReadQualityCount(); + rqc.setBase(Base.REF); + rqc.setQuality(phred); + rqc.setCount(550); + rc.addReadQualityCount(rqc); + countsBuilder.put(position1, rc); + readCounts = countsBuilder.build(); + assertEquals(Precision.compareTo(Solver.maximize( + new LikelihoodFn(readCounts), 0.0, 0.5, 0.05, + 0.0001, 0.0001, 100, 100), 0.1, 0.0001), 0); + } + +} \ No newline at end of file diff --git a/src/test/java/com/google/cloud/genomics/dataflow/utils/VariantFunctionsTest.java b/src/test/java/com/google/cloud/genomics/dataflow/utils/VariantFunctionsTest.java new file mode 100644 index 0000000..31d7a2f --- /dev/null +++ b/src/test/java/com/google/cloud/genomics/dataflow/utils/VariantFunctionsTest.java @@ -0,0 +1,102 @@ +/* + * Copyright (C) 2015 Google Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except + * in compliance with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License + * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express + * or implied. See the License for the specific language governing permissions and limitations under + * the License. + */ +package com.google.cloud.genomics.dataflow.utils; + +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; + +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +import com.google.genomics.v1.Variant; + +/** + * Tests for the VariantUtils class. + */ +@RunWith(JUnit4.class) +public class VariantFunctionsTest { + + @Test + public void testIsPassing() { + // Only success case as stated by VCF 4.2 format. + assertTrue(VariantFunctions.IS_PASSING.apply(Variant.newBuilder() + .addFilter("PASS") + .build())); + // Typical failue case + assertFalse(VariantFunctions.IS_PASSING.apply(Variant.newBuilder() + .addFilter("BAD") + .build())); + // Failue with multiple annotations + assertFalse(VariantFunctions.IS_PASSING.apply(Variant.newBuilder() + .addFilter("BAD") + .addFilter("q<10") + .build())); + // Malformed case; PASS with additional annotations + assertFalse(VariantFunctions.IS_PASSING.apply(Variant.newBuilder() + .addFilter("PASS") + .addFilter("q<10") + .build())); + } + + @Test + public void testIsOnChromosome() { + assertFalse(VariantFunctions.IS_ON_CHROMOSOME.apply(Variant.newBuilder() + .setReferenceName("chrZ") + .build())); + assertTrue(VariantFunctions.IS_ON_CHROMOSOME.apply(Variant.newBuilder() + .setReferenceName("1") + .build())); + } + + @Test + public void testIsNotLowQuality() { + assertFalse(VariantFunctions.IS_NOT_LOW_QUALITY.apply(Variant.newBuilder() + .setQuality(0.0) + .build())); + assertTrue(VariantFunctions.IS_NOT_LOW_QUALITY.apply(Variant.newBuilder() + .setQuality(10.0) + .build())); + } + + @Test + public void testIsSingleAlternateSnp() { + // no alternates + assertFalse(VariantFunctions.IS_SINGLE_ALTERNATE_SNP.apply(Variant.newBuilder() + .setReferenceBases("A") + .build())); + // multiple alternates + assertFalse(VariantFunctions.IS_SINGLE_ALTERNATE_SNP.apply(Variant.newBuilder() + .setReferenceBases("A") + .addAlternateBases("G") + .addAlternateBases("T") + .build())); + // ref too long + assertFalse(VariantFunctions.IS_SINGLE_ALTERNATE_SNP.apply(Variant.newBuilder() + .setReferenceBases("AC") + .addAlternateBases("G") + .build())); + // alternate too long + assertFalse(VariantFunctions.IS_SINGLE_ALTERNATE_SNP.apply(Variant.newBuilder() + .setReferenceBases("A") + .addAlternateBases("GT") + .build())); + // success + assertTrue(VariantFunctions.IS_SINGLE_ALTERNATE_SNP.apply(Variant.newBuilder() + .setReferenceBases("A") + .addAlternateBases("G") + .build())); + } + +} \ No newline at end of file diff --git a/src/test/resources/com/google/cloud/genomics/dataflow/readers/bam/conversion_test.sam b/src/test/resources/com/google/cloud/genomics/dataflow/readers/bam/conversion_test.sam new file mode 100644 index 0000000..aacbba1 --- /dev/null +++ b/src/test/resources/com/google/cloud/genomics/dataflow/readers/bam/conversion_test.sam @@ -0,0 +1,29 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr2 LN:101 +@SQ SN:chr3 LN:101 +@SQ SN:chr4 LN:101 +@SQ SN:chr5 LN:101 +@SQ SN:chr6 LN:101 +@SQ SN:chr7 LN:202 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Momma! LB:whatever PU:me PL:ILLUMINA +SL-XAV:1:1:0:764#0/1 89 chr1 1 255 101M * 0 0 TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN &/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0& RG:Z:0 NN:Z:Hello +SL-XAV:1:1:0:1668#0/2 153 chr2 1 255 101M * 0 0 CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN (/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880& RG:Z:0 NN:Z:Goodbye +SL-XAV:1:1:0:1914#0/2 153 chr3 1 255 101M * 0 0 CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN (0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0& RG:Z:0 +SL-XAV:1:1:0:1639#0/2 153 chr4 1 255 101M * 0 0 CGTGATACCANCTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATATTTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGNTTTGCAGCCN '.&.&&'.0+01'2(1'(''-)','+0041/.+032;:867115/5267-.0/)-5.&-26200224,,0+0/0275/5605688::646875568882*& RG:Z:0 +SL-XAV:1:1:0:68#0/2 137 chr5 1 255 101M * 0 0 NTCTCATTTANAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCANGACGTTATCT &1<<999;;;;<<<87579:556972789977444.'.023.&,7621/54.49.)/53055-22--''+(.'-))6-168/(3&&0(<).))*&&&&&'0 RG:Z:0 +SL-XAV:1:1:0:700#0/2 137 chr6 1 255 101M * 0 0 NAATTGTTCTNAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACNAGTGTCGATC &0::887::::6/646::838388811/679:87640&./2+/-4/28:3,536/4''&&.78/(/554/./02*)*',-(57()&.6(6:(0601'/(,* RG:Z:0 +SL-XAV:1:1:0:1721#0/1 83 chr7 1 255 101M = 102 40 CAACAGAAGGNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCGAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +SL-XAV:1:1:0:105#0/2 403 chr7 1 255 101M = 102 79 CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN /))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.& RG:Z:0 +SL-XAV:1:1:0:1721#0/2 163 chr7 102 255 101M = 1 -40 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +SL-XAV:1:1:0:105#0/2 147 chr8 1 255 101M = 102 79 CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN /))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.& RG:Z:0 +SL-XAV:1:1:0:105#0/1 99 chr8 102 255 101M = 1 -79 NCAGGTTCAANTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA &06665578::41.*/7577/&/77403-324.&&&&&&&&/.&&..&&.0&&&&',:9:/-/(55002020+3'12+2/&.2-&//&),&*&&&&&&&51 RG:Z:0 +SL-XAV:1:1:0:1300#0/1 77 * 0 0 * * 0 0 NAAACACAAGNNANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC &*5535)*-,,&.&.*-1)*,&'&)&1&&.,)&&&&&&&&&)0&&&0'&&&&.&&*2'/4''0/**&)&,'-&*,&,&&&.0.&)&&&**&,.&&&')&&) RG:Z:0 +SL-XAV:1:1:0:1300#0/2 141 * 0 0 * * 0 0 NGATCATGGANGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCANAGTCTCTCAC &&'+''3*&-/)/1'26/*-2-/542-*&-&/'/*/&-'&)-')&.'-/&&2+122*'&+,(/-&)((,/-,,.'2(2'+)/&/&-66-&&/16&)&*&'3 RG:Z:0 +SL-XAV:1:1:0:1639#0/1 101 * 0 0 * chr1 1 0 NCCCTCTCAGNNTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG &1::::::64/&/&0:3.280&/&087881,/&&&&&&&&&..&&&..&,,&-&&,265341-)/5680&-.5552-25/322/42/&)&&).421&-&-/ RG:Z:0 +SL-XAV:1:1:0:1668#0/1 101 * 0 0 * chr2 1 0 NATAGCATACNNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC &1988998890&0&.8863//&.&.0-2875.&&&&&&&&&.)&&&..&.&&.&&.5782-2+262)&-0-0510*.332-2.-,0*&&*&'.&-2-)0., RG:Z:0 +SL-XAV:1:1:0:1914#0/1 101 * 0 0 * chr3 1 0 NTTTTTCTCCNNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG &0::::<<;90&/&.244760&,&.414798/&&&&&&&&&00&&&0.&/&&-&&.4475687363504.&.557/.*)65.&/*./&&.&.+*)&..).& RG:Z:0 +SL-XAV:1:1:0:68#0/1 581 * 0 0 * chr4 1 0 NAATATTCATNNGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA &0<<:::::