[pkgsrc/trunk]: pkgsrc/biology bcftools: added version 1.9

[adam <adam%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/38de20af27de
branches:  trunk
changeset: 387341:38de20af27de
user:      adam <adam%pkgsrc.org@localhost>
date:      Thu Nov 15 09:21:24 2018 +0000

description:
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.

diffstat:

 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 deletions(-)

diffs (114 lines):

diff -r 1427810b5901 -r 38de20af27de biology/Makefile
--- a/biology/Makefile  Thu Nov 15 08:46:35 2018 +0000
+++ b/biology/Makefile  Thu Nov 15 09:21:24 2018 +0000
@@ -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 -r 1427810b5901 -r 38de20af27de biology/bcftools/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/bcftools/DESCR    Thu Nov 15 09:21:24 2018 +0000
@@ -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 -r 1427810b5901 -r 38de20af27de biology/bcftools/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/bcftools/Makefile Thu Nov 15 09:21:24 2018 +0000
@@ -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=        ${PKGVERSION_NOREV}
+
+MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=      http://samtools.github.io/bcftools/
+COMMENT=       Calling and manipulating files VCF and BCF formats
+LICENSE=       mit
+
+USE_TOOLS+=            gmake perl
+GNU_CONFIGURE=         yes
+CONFIGURE_ARGS+=       --with-htslib=system
+TEST_TARGET=           test
+
+BUILDLINK_TRANSFORM+=   opt:-ldl:${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 -r 1427810b5901 -r 38de20af27de biology/bcftools/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/bcftools/PLIST    Thu Nov 15 09:21:24 2018 +0000
@@ -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 -r 1427810b5901 -r 38de20af27de biology/bcftools/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/bcftools/distinfo Thu Nov 15 09:21:24 2018 +0000
@@ -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