svn commit: r569033 - in head/biology: . ad2vcf

[Jason W. Bacon]

Author: jwb
Date: Tue Mar 23 15:15:00 2021
New Revision: 569033
URL: https://svnweb.freebsd.org/changeset/ports/569033

Log:
  biology/ad2vcf: Add allelic depth info from a SAM stream to a VCF file
  
  ad2vdf extracts allelic depth info from a SAM stream and adds it to a
  corresponding single-sample VCF file.  SAM input is read via stdin and the VCF
  input file is taken as a command-line argument. This allows expensive BAM/CRAM
  decoding to be performed in parallel by a separate samtools process.

Added:
  head/biology/ad2vcf/
  head/biology/ad2vcf/Makefile   (contents, props changed)
  head/biology/ad2vcf/distinfo   (contents, props changed)
  head/biology/ad2vcf/pkg-descr   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Tue Mar 23 15:06:07 2021	(r569032)
+++ head/biology/Makefile	Tue Mar 23 15:15:00 2021	(r569033)
@@ -4,6 +4,7 @@
     COMMENT = Biology
 
     SUBDIR += abyss
+    SUBDIR += ad2vcf
     SUBDIR += artemis
     SUBDIR += avida
     SUBDIR += babel

Added: head/biology/ad2vcf/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/ad2vcf/Makefile	Tue Mar 23 15:15:00 2021	(r569033)
@@ -0,0 +1,26 @@
+# $FreeBSD$
+
+PORTNAME=	ad2vcf
+DISTVERSION=	0.1.2
+CATEGORIES=	biology
+
+MAINTAINER=	jwb at FreeBSD.org
+COMMENT=	Add allelic depth info from a SAM stream to a VCF file
+
+LICENSE=	BSD2CLAUSE
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	biolibc>=0.1.1:biology/biolibc
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	auerlab
+
+PLIST_FILES=	bin/ad2vcf man/man1/ad2vcf.1.gz
+
+pre-build:
+	(cd ${WRKSRC} && ${MAKE} LOCALBASE=${LOCALBASE} depend)
+
+do-test:
+	(cd ${WRKSRC}/Test && ./run-test.sh)
+
+.include <bsd.port.mk>

Added: head/biology/ad2vcf/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/ad2vcf/distinfo	Tue Mar 23 15:15:00 2021	(r569033)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1616510305
+SHA256 (auerlab-ad2vcf-0.1.2_GH0.tar.gz) = e85e221c69748082799f5b048412136d28a0395290b16728500fe30190eaea84
+SIZE (auerlab-ad2vcf-0.1.2_GH0.tar.gz) = 15204

Added: head/biology/ad2vcf/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/ad2vcf/pkg-descr	Tue Mar 23 15:15:00 2021	(r569033)
@@ -0,0 +1,6 @@
+ad2vdf extracts allelic depth info from a SAM stream and adds it to a
+corresponding single-sample VCF file.  SAM input is read via stdin and the VCF
+input file is taken as a command-line argument. This allows expensive BAM/CRAM
+decoding to be performed in parallel by a separate samtools process.
+
+WWW: https://github.com/auerlab/ad2vcf