prep for release

README.md

@@ -6,14 +6,14 @@
 Echtvar enables rapid annotation of variants with huge pupulation datasets and
 it supports filtering on those values. It chunks the genome into 1<<20 (~1 million
 ) bases, [encodes each variant into a 32 bit integer](https://github.com/brentp/echtvar/blob/02774b8d1cd3703b65bd2c8d7aab93af05b7940f/src/lib/var32.rs#L9-L21) (with a [supplemental table](https://github.com/brentp/echtvar/blob/02774b8d1cd3703b65bd2c8d7aab93af05b7940f/src/lib/var32.rs#L33-L38)
-for those that can't fit due to large REF and/or ALT alleles). It uses [delta
+for those that can't fit due to large REF and/or ALT alleles). It uses the zip format, [delta
 encoding](https://en.wikipedia.org/wiki/Delta_encoding)
 and [integer compression
 ](https://lemire.me/blog/2017/09/27/stream-vbyte-breaking-new-speed-records-for-integer-compression/)
 to create a compact and searchable format of any integer or float columns
 selected from the population file.
 
-Once created, an echtvar file can be used to annotate variants in a VCF (or
+Once created, an echtvar (zip) file can be used to annotate variants in a VCF (or
 BCF) file at a rate of >1 million variants per second (most of the time is spent
 reading and writing VCF/BCF, so this number depends on the particular file).
 
@@ -29,7 +29,7 @@ and then the file can be re-used for the `annotate` step with each new query fil
 ```
 echtvar \
    encode \
-   echtvar-gnomad-v3.zip \
+   gnomad.v3.1.2.echtvar.zip \
    conf.json # this defines the columns to pull from $input_vcf, and how to
    $input_population_vcf[s] \ can be split by chromosome or all in a single file.
 name and encode them
@@ -39,14 +39,19 @@ name and encode them
 See below for a description of the json file that defines which columns are
 pulled from the population VCF.
 
+> you can get a pre-made 6.8GB echtvar file from gnomad v3.1.2 (hg38 whole genomes) with this command:
+> ```
+> curl -L -o gnomad.v3.1.2.echtvar.zip https://surfdrive.surf.nl/files/index.php/s/O4mehMM7b3cmK9s/download
+> ```
+
 annotate a VCF with an echtvar file and only output variants where `gnomad_af`
 from the echtvar file is < 0.01.
 
 ```
 echtvar annotate \
-   -o $cohort.echtvar-annotated.bcf \
-   -a gnomad.echtvar \
-   -i 'gnomad_af < 0.01' \
+   -o $cohort.echtvar-annotated.filtered.bcf \
+   -a gnomad.v3.1.2.echtvar.zip \
+   -i 'gnomad_popmax_af < 0.01' \
    $cohort.input.bcf
 ```
 

examples/gnomad.v3.1.2.json

@@ -0,0 +1,18 @@
+// this it the file used to create the files linked from echtvar releases.
+// when using that echtvar file, each of the "aliases" listed here will be added
+// to the output file.
+[
+        {"field": "AC", "alias": "gnomad_ac"},
+        {"field": "AN", "alias": "gnomad_an"},
+        {"field": "nhomalt", "alias": "gnomad_nhomalt"},
+        {"field": "AF", "alias": "gnomad_af", multiplier: 2000000},
+
+        {"field": "AC_popmax", "alias": "gnomad_popmax_ac"},
+        {"field": "AN_popmax", "alias": "gnomad_popmax_an"},
+        {"field": "nhomalt_popmax", "alias": "gnomad_popmax_nhomalt"},
+        {"field": "AF_popmax", "alias": "gnomad_popmax_af", multiplier: 2000000},
+
+        {"field": "AF_controls_and_biobanks", "alias": "gnomad_controls_and_biobanks_af", multiplier: 2000000},
+        {"field": "nhomalt_controls_and_biobanks", "alias": "gnomad_controls_and_biobanks_nhomalt"},
+]
+

src/main.rs

@@ -8,13 +8,13 @@ extern crate fasteval;
 use commands::{annotate_cmd, encoder_cmd};
 use std::error::Error;
 
-const VERSION: &str = "0.0.1";
+const VERSION: &str = env!("CARGO_PKG_VERSION");
 
 fn main() -> Result<(), Box<dyn Error>> {
     let mut app = clap_app!(echtvar =>
         (version: VERSION)
         (author: "Brent Pedersen <[email protected]")
-        (about:"variant encoding and annotation")
+        (about: "variant encoding and annotation")
         (@subcommand encode =>
             (about: "create an echtvar file from a population VCF/BCF")
             (@arg OUTPUT: +required "output zip file")