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| author | bacon <bacon@pkgsrc.org> | 2021-03-24 15:22:29 +0000 |
|---|---|---|
| committer | bacon <bacon@pkgsrc.org> | 2021-03-24 15:22:29 +0000 |
| commit | dfe56e923f7ad16e6a1a908656cba9b35c871dcc (patch) | |
| tree | 7fac110667f6b880cf6e4c2a4e634c564c558bd9 /biology | |
| parent | 1181a4b0eb00eab64cac8aa0c9447cafa1308140 (diff) | |
| download | pkgsrc-dfe56e923f7ad16e6a1a908656cba9b35c871dcc.tar.gz | |
biology/vcf-split: import vcf-split-0.1.1
Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands
of output files simultaneously. Parsing the TOPMed human chromosome 1 BCF
with bcftools takes two days, so extracting the 137,977 samples one at a time
or using thousands of parallel readers of the same file is impractical.
Vcf-split solves this by generating thousands of single-sample outputs during
a single sweep through the multi-sample input.
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/vcf-split/DESCR | 6 | ||||
| -rw-r--r-- | biology/vcf-split/Makefile | 16 | ||||
| -rw-r--r-- | biology/vcf-split/PLIST | 3 | ||||
| -rw-r--r-- | biology/vcf-split/distinfo | 6 |
4 files changed, 31 insertions, 0 deletions
diff --git a/biology/vcf-split/DESCR b/biology/vcf-split/DESCR new file mode 100644 index 00000000000..37f7d39c7c9 --- /dev/null +++ b/biology/vcf-split/DESCR @@ -0,0 +1,6 @@ +Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands +of output files simultaneously. Parsing the TOPMed human chromosome 1 BCF +with bcftools takes two days, so extracting the 137,977 samples one at a time +or using thousands of parallel readers of the same file is impractical. +Vcf-split solves this by generating thousands of single-sample outputs during +a single sweep through the multi-sample input. diff --git a/biology/vcf-split/Makefile b/biology/vcf-split/Makefile new file mode 100644 index 00000000000..3b3285dfba0 --- /dev/null +++ b/biology/vcf-split/Makefile @@ -0,0 +1,16 @@ +# $NetBSD: Makefile,v 1.1 2021/03/24 15:22:29 bacon Exp $ + +DISTNAME= vcf-split-0.1.1 +CATEGORIES= biology +MASTER_SITES= ${MASTER_SITE_GITHUB:=auerlab/} + +MAINTAINER= bacon@NetBSD.org +HOMEPAGE= https://github.com/auerlab/vcf-split +COMMENT= Split a multi-sample VCF into single-sample VCFs +LICENSE= 2-clause-bsd + +pre-build: + cd ${WRKSRC} && ${MAKE} PREFIX=${PREFIX} depend + +.include "../../biology/biolibc/buildlink3.mk" +.include "../../mk/bsd.pkg.mk" diff --git a/biology/vcf-split/PLIST b/biology/vcf-split/PLIST new file mode 100644 index 00000000000..0efca2992ad --- /dev/null +++ b/biology/vcf-split/PLIST @@ -0,0 +1,3 @@ +@comment $NetBSD: PLIST,v 1.1 2021/03/24 15:22:29 bacon Exp $ +bin/vcf-split +man/man1/vcf-split.1 diff --git a/biology/vcf-split/distinfo b/biology/vcf-split/distinfo new file mode 100644 index 00000000000..d11adf9a848 --- /dev/null +++ b/biology/vcf-split/distinfo @@ -0,0 +1,6 @@ +$NetBSD: distinfo,v 1.1 2021/03/24 15:22:29 bacon Exp $ + +SHA1 (vcf-split-0.1.1.tar.gz) = 550fefb4c07d4632405e94127a19e98031ac0067 +RMD160 (vcf-split-0.1.1.tar.gz) = 76a1b0b5a8934949d39e69ebe719c8f0ba247a13 +SHA512 (vcf-split-0.1.1.tar.gz) = fcc67d287adb9b1f12fb316981ca0b0c06099d8de07113760d198fbcbafb2557ae0d1c202976fae98d6d712a7b802728979d8224354fbaaf65a7872a27d1aa00 +Size (vcf-split-0.1.1.tar.gz) = 14226 bytes |