From 3105bda4648695eec2d2ea189258407215990d55 Mon Sep 17 00:00:00 2001 From: adam Date: Thu, 15 Nov 2018 09:21:24 +0000 Subject: bcftools: added version 1.9 BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. In order to avoid tedious repetion, throughout this document we will use "VCF" and "BCF" interchangeably, unless specifically noted. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF work in all situations. Unindexed VCF and BCF and streams work in most, but not all situations. In general, whenever multiple VCFs are read simultaneously, they must be indexed and therefore also compressed. --- biology/Makefile | 3 ++- biology/bcftools/DESCR | 11 +++++++++++ biology/bcftools/Makefile | 28 ++++++++++++++++++++++++++++ biology/bcftools/PLIST | 37 +++++++++++++++++++++++++++++++++++++ biology/bcftools/distinfo | 6 ++++++ 5 files changed, 84 insertions(+), 1 deletion(-) create mode 100644 biology/bcftools/DESCR create mode 100644 biology/bcftools/Makefile create mode 100644 biology/bcftools/PLIST create mode 100644 biology/bcftools/distinfo diff --git a/biology/Makefile b/biology/Makefile index f1f5d9da485..ed53c70e1e9 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,10 +1,11 @@ -# $NetBSD: Makefile,v 1.47 2018/10/31 20:16:30 leot Exp $ +# $NetBSD: Makefile,v 1.48 2018/11/15 09:21:24 adam Exp $ # COMMENT= Software for the biological sciences SUBDIR+= arka SUBDIR+= azara +SUBDIR+= bcftools SUBDIR+= bioperl SUBDIR+= bodr SUBDIR+= bwa diff --git a/biology/bcftools/DESCR b/biology/bcftools/DESCR new file mode 100644 index 00000000000..9cc66419380 --- /dev/null +++ b/biology/bcftools/DESCR @@ -0,0 +1,11 @@ +BCFtools is a program for variant calling and manipulating files in the Variant +Call Format (VCF) and its binary counterpart BCF. All commands work +transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. +In order to avoid tedious repetion, throughout this document we will use "VCF" +and "BCF" interchangeably, unless specifically noted. + +Most commands accept VCF, bgzipped VCF and BCF with filetype detected +automatically even when streaming from a pipe. Indexed VCF and BCF work in all +situations. Unindexed VCF and BCF and streams work in most, but not all +situations. In general, whenever multiple VCFs are read simultaneously, they +must be indexed and therefore also compressed. diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile new file mode 100644 index 00000000000..003ad41442f --- /dev/null +++ b/biology/bcftools/Makefile @@ -0,0 +1,28 @@ +# $NetBSD: Makefile,v 1.1 2018/11/15 09:21:24 adam Exp $ + +DISTNAME= bcftools-1.9 +CATEGORIES= biology +MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/} +EXTRACT_SUFX= .tar.bz2 +GITHUB_RELEASE= ${PKGVERSION_NOREV} + +MAINTAINER= pkgsrc-users@NetBSD.org +HOMEPAGE= http://samtools.github.io/bcftools/ +COMMENT= Calling and manipulating files VCF and BCF formats +LICENSE= mit + +USE_TOOLS+= gmake perl +GNU_CONFIGURE= yes +CONFIGURE_ARGS+= --with-htslib=system +TEST_TARGET= test + +BUILDLINK_TRANSFORM+= opt:-ldl:${BUILDLINK_LDADD.dl:M*} + +REPLACE_PERL+= misc/*.pl +REPLACE_PERL+= misc/plot-vcfstats +REPLACE_PYTHON+= misc/*.py + +.include "../../biology/htslib/buildlink3.mk" +.include "../../lang/python/application.mk" +.include "../../mk/dlopen.buildlink3.mk" +.include "../../mk/bsd.pkg.mk" diff --git a/biology/bcftools/PLIST b/biology/bcftools/PLIST new file mode 100644 index 00000000000..42d4cf8a43f --- /dev/null +++ b/biology/bcftools/PLIST @@ -0,0 +1,37 @@ +@comment $NetBSD: PLIST,v 1.1 2018/11/15 09:21:24 adam Exp $ +bin/bcftools +bin/color-chrs.pl +bin/guess-ploidy.py +bin/plot-roh.py +bin/plot-vcfstats +bin/run-roh.pl +bin/vcfutils.pl +libexec/bcftools/GTisec.so +libexec/bcftools/GTsubset.so +libexec/bcftools/ad-bias.so +libexec/bcftools/af-dist.so +libexec/bcftools/check-ploidy.so +libexec/bcftools/check-sparsity.so +libexec/bcftools/color-chrs.so +libexec/bcftools/contrast.so +libexec/bcftools/counts.so +libexec/bcftools/dosage.so +libexec/bcftools/fill-AN-AC.so +libexec/bcftools/fill-from-fasta.so +libexec/bcftools/fill-tags.so +libexec/bcftools/fixploidy.so +libexec/bcftools/fixref.so +libexec/bcftools/frameshifts.so +libexec/bcftools/guess-ploidy.so +libexec/bcftools/impute-info.so +libexec/bcftools/isecGT.so +libexec/bcftools/mendelian.so +libexec/bcftools/missing2ref.so +libexec/bcftools/prune.so +libexec/bcftools/setGT.so +libexec/bcftools/smpl-stats.so +libexec/bcftools/split.so +libexec/bcftools/tag2tag.so +libexec/bcftools/trio-stats.so +libexec/bcftools/trio-switch-rate.so +man/man1/bcftools.1 diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo new file mode 100644 index 00000000000..1aa4f7523f8 --- /dev/null +++ b/biology/bcftools/distinfo @@ -0,0 +1,6 @@ +$NetBSD: distinfo,v 1.1 2018/11/15 09:21:24 adam Exp $ + +SHA1 (bcftools-1.9.tar.bz2) = 9b649c3f407528ee193210f68b8e21e8b0aebf31 +RMD160 (bcftools-1.9.tar.bz2) = 59b9997aaa509ba84c41b7e78821f31eca8d90dc +SHA512 (bcftools-1.9.tar.bz2) = fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c +Size (bcftools-1.9.tar.bz2) = 3134355 bytes -- cgit v1.2.3