CVS commit: pkgsrc/biology/vcf-split

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Wed Mar 24 15:22:29 UTC 2021

Added Files:
        pkgsrc/biology/vcf-split: DESCR Makefile PLIST distinfo

Log Message:
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.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/vcf-split/DESCR \
    pkgsrc/biology/vcf-split/Makefile pkgsrc/biology/vcf-split/PLIST \
    pkgsrc/biology/vcf-split/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/biology/vcf-split/DESCR
diff -u /dev/null pkgsrc/biology/vcf-split/DESCR:1.1
--- /dev/null   Wed Mar 24 15:22:29 2021
+++ pkgsrc/biology/vcf-split/DESCR      Wed Mar 24 15:22:29 2021
@@ -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.
Index: pkgsrc/biology/vcf-split/Makefile
diff -u /dev/null pkgsrc/biology/vcf-split/Makefile:1.1
--- /dev/null   Wed Mar 24 15:22:29 2021
+++ pkgsrc/biology/vcf-split/Makefile   Wed Mar 24 15:22:29 2021
@@ -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@localhost
+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"
Index: pkgsrc/biology/vcf-split/PLIST
diff -u /dev/null pkgsrc/biology/vcf-split/PLIST:1.1
--- /dev/null   Wed Mar 24 15:22:29 2021
+++ pkgsrc/biology/vcf-split/PLIST      Wed Mar 24 15:22:29 2021
@@ -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
Index: pkgsrc/biology/vcf-split/distinfo
diff -u /dev/null pkgsrc/biology/vcf-split/distinfo:1.1
--- /dev/null   Wed Mar 24 15:22:29 2021
+++ pkgsrc/biology/vcf-split/distinfo   Wed Mar 24 15:22:29 2021
@@ -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