svn commit: r568922 - in head/biology: . vcf-split
Jason W. Bacon
jwb at FreeBSD.org
Sun Mar 21 15:17:29 UTC 2021
Author: jwb
Date: Sun Mar 21 15:17:27 2021
New Revision: 568922
URL: https://svnweb.freebsd.org/changeset/ports/568922
Log:
biology/vcf-split: Split a multi-sample VCF into single-sample VCFs
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.
Added:
head/biology/vcf-split/
head/biology/vcf-split/Makefile (contents, props changed)
head/biology/vcf-split/distinfo (contents, props changed)
head/biology/vcf-split/pkg-descr (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Sun Mar 21 15:10:17 2021 (r568921)
+++ head/biology/Makefile Sun Mar 21 15:17:27 2021 (r568922)
@@ -179,6 +179,7 @@
SUBDIR += trimadap
SUBDIR += trimmomatic
SUBDIR += ugene
+ SUBDIR += vcf-split
SUBDIR += vcflib
SUBDIR += vcftools
SUBDIR += velvet
Added: head/biology/vcf-split/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/vcf-split/Makefile Sun Mar 21 15:17:27 2021 (r568922)
@@ -0,0 +1,23 @@
+# $FreeBSD$
+
+PORTNAME= vcf-split
+DISTVERSION= 0.1.1
+CATEGORIES= biology
+
+MAINTAINER= jwb at FreeBSD.org
+COMMENT= Split a multi-sample VCF into single-sample VCFs
+
+LICENSE= BSD2CLAUSE
+LICENSE_FILE= ${WRKSRC}/LICENSE
+
+BUILD_DEPENDS= biolibc>=0.1.1:biology/biolibc
+
+USE_GITHUB= yes
+GH_ACCOUNT= auerlab
+
+PLIST_FILES= bin/vcf-split man/man1/vcf-split.1.gz
+
+pre-build:
+ (cd ${WRKSRC} && ${MAKE} LOCALBASE=${LOCALBASE} depend)
+
+.include <bsd.port.mk>
Added: head/biology/vcf-split/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/vcf-split/distinfo Sun Mar 21 15:17:27 2021 (r568922)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1616331493
+SHA256 (auerlab-vcf-split-0.1.1_GH0.tar.gz) = 07fb3aff5bf6038b251baa6c0cbff0600487766838b497468ab06d300488f310
+SIZE (auerlab-vcf-split-0.1.1_GH0.tar.gz) = 14226
Added: head/biology/vcf-split/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/vcf-split/pkg-descr Sun Mar 21 15:17:27 2021 (r568922)
@@ -0,0 +1,8 @@
+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.
+
+WWW: https://github.com/auerlab/vcf-split
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