svn commit: r568922 - in head/biology: . vcf-split

[Jason W. Bacon]

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