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Bacon" Date: Tue, 23 Mar 2021 15:15:01 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r569033 - in head/biology: . ad2vcf X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology: . ad2vcf X-SVN-Commit-Revision: 569033 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 23 Mar 2021 15:15:02 -0000 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@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 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