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.

5 files changed, 84 insertions, 1 deletions

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