[pkgsrc/trunk]: pkgsrc/biology/vcf-split biology/vcf-split: import vcf-split-...

[bacon <bacon%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/6b7b55ec8400
branches:  trunk
changeset: 449267:6b7b55ec8400
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Wed Mar 24 15:22:29 2021 +0000

description:
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:

 biology/vcf-split/DESCR    |   6 ++++++
 biology/vcf-split/Makefile |  16 ++++++++++++++++
 biology/vcf-split/PLIST    |   3 +++
 biology/vcf-split/distinfo |   6 ++++++
 4 files changed, 31 insertions(+), 0 deletions(-)

diffs (47 lines):

diff -r fa9562142304 -r 6b7b55ec8400 biology/vcf-split/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/vcf-split/DESCR   Wed Mar 24 15:22:29 2021 +0000
@@ -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 -r fa9562142304 -r 6b7b55ec8400 biology/vcf-split/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/vcf-split/Makefile        Wed Mar 24 15:22:29 2021 +0000
@@ -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"
diff -r fa9562142304 -r 6b7b55ec8400 biology/vcf-split/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/vcf-split/PLIST   Wed Mar 24 15:22:29 2021 +0000
@@ -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 -r fa9562142304 -r 6b7b55ec8400 biology/vcf-split/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/vcf-split/distinfo        Wed Mar 24 15:22:29 2021 +0000
@@ -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