Merge pull request #84 from ARUP-NGS/dev

Dev merge for 1.0.3

Makefile

@@ -8,8 +8,8 @@ CXXSTD=c++11
 CSTD=gnu99
 CC=g++
 GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always)
-CFLAGS= -Wunreachable-code -Wall -fopenmp -DBMF_VERSION=\"$(GIT_VERSION)\" -std=$(CSTD) -fno-builtin-gamma -pedantic
-FLAGS= -Wunreachable-code -Wall -fopenmp -DBMF_VERSION=\"$(GIT_VERSION)\" -std=$(CXXSTD) -fno-builtin-gamma -pedantic
+CFLAGS= -Wuninitialized -Wunreachable-code -Wall -fopenmp -DBMF_VERSION=\"$(GIT_VERSION)\" -std=$(CSTD) -fno-builtin-gamma -pedantic
+FLAGS= -Wuninitialized -Wunreachable-code -Wall -fopenmp -DBMF_VERSION=\"$(GIT_VERSION)\" -std=$(CXXSTD) -fno-builtin-gamma -pedantic  # -Weffc++
 LD= -lm -lz -lpthread
 INCLUDE= -Ihtslib -Iinclude -I.
 LIB=
@@ -30,9 +30,9 @@ DLIB_SRC = dlib/cstr_util.c dlib/math_util.c dlib/vcf_util.c dlib/io_util.c dlib
 
 SOURCES = include/sam_opts.c src/bmf_dmp.c include/igamc_cephes.c src/bmf_hashdmp.c \
           src/bmf_sdmp.c src/bmf_rsq.c src/bmf_famstats.c include/bedidx.c \
-          src/bmf_err.c src/bmf_infer.c\
+          src/bmf_err.c \
           lib/kingfisher.c src/bmf_mark.c src/bmf_cap.c lib/mseq.c lib/splitter.c \
-          src/bmf_main.c src/bmf_target.c src/bmf_depth.c src/bmf_vetter.c src/bmf_sort.c src/bmf_stack.c \
+          src/bmf_main.c src/bmf_target.c src/bmf_depth.c src/bmf_vet.c src/bmf_sort.c src/bmf_stack.c \
           lib/stack.c src/bmf_filter.c $(DLIB_SRC)
 
 TEST_SOURCES = test/target_test.c test/ucs/ucs_test.c test/tag/array_tag_test.c
@@ -95,7 +95,7 @@ tag_test: $(OBJS) $(TEST_OBJS) libhts.a
 target_test: $(D_OBJS) $(TEST_OBJS) libhts.a
 	$(CC) $(FLAGS) $(DB_FLAGS) $(INCLUDE) $(LIB) $(LD) dlib/bed_util.dbo src/bmf_target.dbo test/target_test.dbo libhts.a -o ./target_test && ./target_test
 hashdmp_test: $(BINS)
-	cd test/dmp && python hashdmp_test.py && cd ../..
+	cd test/collapse && python hashdmp_test.py && cd ../..
 marksplit_test: $(BINS)
 	cd test/marksplit && python marksplit_test.py && cd ../..
 err_test: $(BINS)

README.md

@@ -37,14 +37,10 @@ Name | Use |
 :---:|:----|
 bmftools cap| Postprocess a tagged BAM for BMF-agnostic tools.|
 bmftools depth| Calculates depth of coverage over a set of bed intervals.|
-bmftools dmp| Demultiplex inline barcoded experiments.|
+bmftools collapse| Collapse initial fastq records by barcode|
 bmftools err| Calculate error rates based on cycle, base call, and quality score.|
 bmftools famstats| Calculate family size statistics for a bam alignment file.|
 bmftools filter| Filter or split a bam file by a set of filters.|
-bmftools mark| Add unclipped start position as annotation for both read and mate.|
-bmftools rsq| Rescue bmf-sorted or ucs-sorted bam alignments.|
-bmftools sdmp| Demultiplex secondary-index barcoded experiments.|
-bmftools sort| Sort for bam rescue.|
 bmftools stack| A maximally-permissive variant caller using molecular barcode metadata analogous to samtools mpileup.|
 bmftools target| Calculates on-target rate.|
 bmftools vet| Curate variant calls from another variant caller (.bcf) and a bam alignment.|
@@ -53,27 +49,16 @@ These tools are divided into four categories:
   1. Core functionality
   2. Manipulation
   3. Analysis
-  4. Utilities
 
 ### Core Functionality
 
-####bmftools dmp/sdmp
-bmftools dmp and sdmp perform **molecular** demultiplexing of barcoded experiments, for inline and secondary index chemistries, respectively.
+####bmftools collapse
+bmftools collapse combines reads sharing barcodes into single observations respectively.
 
-First, these tools add the barcodes to the comment fields of the fastqs and split the records into subsets based on the first characters in the barcode.
-Then, reads with exactly-matching barcode are collapsed into a unique observation, with a meta-analysis performed on each base call.
+First, the barcodes are added to the comment fields of the fastqs and split the records into subsets based on the first characters in the barcode.
+Then, reads with exactly-matching barcode are collapsed, with a meta-analysis performed on each base call.
 
-Since there can be errors in reading the barcode,
-`bmftools rsq` is made available for using positional information to rescue reads with mismatches into their proper families.
-
-bmftools dmp collapses templates where both strands were sequenced, whereas sdmp lacks strand information.
-
-Note: It is **STRONGLY** recommended that for the secondary-index chemistry that you mask adapter sequence in the molecular barcode reads.
-When the secondary-index barcode read consists primarily or entirely of adapter, this informs us that the chemistry did not perform as expected.
-This preprocessing will "N" those bases, marking the reads as QC fail with the FP integer tag (0 for fail, 1 for pass).
-
-####bmftools rsq
-Uses positional information to collapse reads with the same alignment signatures (start/stop/
+bmftools collapse inline collapses templates where both strands were sequenced, whereas collapse secondary lacks strand information.
 
 ### Manipulation
 
@@ -109,35 +94,23 @@ Calculates on-target fraction for bed file using barcode metadata.
 
 ####bmftools err
 Calculates error rates by a variety of parameters.
-Additionally, pre-computes the quality score recalibration for the optional dmp/sdmp recalibration step.
+Additionally, pre-computes the quality score recalibration for the optional collapse recalibration step.
 
 ####bmftools famstats
 Calculates summary statistics related to family size and demultiplexing.
 
 ####bmftools stack
 A maximally-permissive variant caller using molecular barcode metadata analogous to samtools mpileup.
 
-### Utilities
-
-####bmftools mark
-Adds auxiliary tags to reads for their mates' information. Required for bmftools rsq.
-
-####bmftools sort
-Sorts reads based on positional information to preprocess for bmftools rsq.
-
 
 ## BMF Tags
 
 Tag | Content | Format |
 :----:|:-----|:-----:|
-DR | Whether the read was sequenced from both strands. Only valid for Loeb-like inline barcodes. | Integer [0, 1] |
+DR | Whether the read was sequenced from both strands. Only valid for inline chemistry. | Integer [0, 1] |
 FA | Number of reads in Family which Agreed with final sequence at each base | uint32_t array |
 FM | Size of family (number of reads sharing barcode.), e.g., "Family Members" | Integer |
 FP | Read Passes Filter related to barcoding. Determines QC fail flag in bmftools mark (without -q).| Integer [0, 1]|
-LM | Length of Mate | Integer |
-MF | Mate fraction aligned (fraction of bases mapped to reference bases, not counting IDSHNP operations. | Float |
-NC | Number of changed bases in rescued families of reads. | Integer |
 NF | Mean number of differences between reads and consensus per read in family | Float |
-NP | Number of Pre-rescue reads. Number of reads before rescue in a final post-rescue observation. | Integer |
 PV | Phred Values for a base call after meta-analysis | uint32_t array |
-RV | Number of reversed reads in consensus. Only for Loeb-style inline chemistry. | Integer |
+RV | Number of reversed reads in consensus. Only for inline chemistry. | Integer |