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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-03-23 15:15:00 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-03-23 15:15:00 +0000 |
| commit | aa8e14f1c183bdc57940de974b9773b498595974 (patch) | |
| tree | 8975f218155bc5451f968db6b12d5b18b128f803 /biology | |
| parent | d20299d14c70387e5f3f69ebbdacee90272809a1 (diff) | |
| download | ports-aa8e14f1c183bdc57940de974b9773b498595974.tar.gz ports-aa8e14f1c183bdc57940de974b9773b498595974.zip | |
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.
Notes
Notes:
svn path=/head/; revision=569033
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/ad2vcf/Makefile | 26 | ||||
| -rw-r--r-- | biology/ad2vcf/distinfo | 3 | ||||
| -rw-r--r-- | biology/ad2vcf/pkg-descr | 6 |
4 files changed, 36 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index cba970a40784..260d2763d896 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -4,6 +4,7 @@ COMMENT = Biology SUBDIR += abyss + SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel diff --git a/biology/ad2vcf/Makefile b/biology/ad2vcf/Makefile new file mode 100644 index 000000000000..e3703746263e --- /dev/null +++ b/biology/ad2vcf/Makefile @@ -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 <bsd.port.mk> diff --git a/biology/ad2vcf/distinfo b/biology/ad2vcf/distinfo new file mode 100644 index 000000000000..649dbb04a74c --- /dev/null +++ b/biology/ad2vcf/distinfo @@ -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 diff --git a/biology/ad2vcf/pkg-descr b/biology/ad2vcf/pkg-descr new file mode 100644 index 000000000000..21df7c875513 --- /dev/null +++ b/biology/ad2vcf/pkg-descr @@ -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 |