samtools: Import from biology for repair, cleanup and testing

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Feb 15 16:19:40 2019 -0600
Changeset:	c937d85e781b82b341dd6490d80a22118da29644

Modified Files:
	Makefile
Added Files:
	samtools/DESCR
	samtools/Makefile
	samtools/PLIST
	samtools/TODO
	samtools/distinfo

Log Message:
samtools: Import from biology for repair, cleanup and testing

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c937d85e781b82b341dd6490d80a22118da29644

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile          |  1 +
 samtools/DESCR    |  3 +++
 samtools/Makefile | 28 ++++++++++++++++++++++++++++
 samtools/PLIST    | 24 ++++++++++++++++++++++++
 samtools/TODO     |  3 +++
 samtools/distinfo |  6 ++++++
 6 files changed, 65 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index d8b796f5e5..e09293771b 100644
--- a/Makefile
+++ b/Makefile
@@ -4257,6 +4257,7 @@ SUBDIR+=	sais
 SUBDIR+=	sais-demo-data
 SUBDIR+=	salmon
 SUBDIR+=	samhain
+SUBDIR+=	samtools
 SUBDIR+=	samtools0119
 SUBDIR+=	sara
 SUBDIR+=	sarf
diff --git a/samtools/DESCR b/samtools/DESCR
new file mode 100644
index 0000000000..23d11d1c81
--- /dev/null
+++ b/samtools/DESCR
@@ -0,0 +1,3 @@
+Samtools implements various utilities for post-processing alignments in the
+SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
+with bcftools), and a simple alignment viewer.
diff --git a/samtools/Makefile b/samtools/Makefile
new file mode 100644
index 0000000000..7fece1543a
--- /dev/null
+++ b/samtools/Makefile
@@ -0,0 +1,28 @@
+# $NetBSD: Makefile,v 1.3 2018/11/06 10:49:41 adam Exp $
+
+DISTNAME=	samtools-1.9
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
+EXTRACT_SUFX=	.tar.bz2
+GITHUB_RELEASE=	${PKGVERSION_NOREV}
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	http://www.htslib.org/
+COMMENT=	Tools for manipulating next-generation sequencing data
+LICENSE=	mit
+
+USE_TOOLS+=		gmake perl:run
+GNU_CONFIGURE=		yes
+CONFIGURE_ARGS+=	--with-htslib=system
+TEST_TARGET=		test
+
+REPLACE_PERL=		misc/*.pl
+REPLACE_PERL+=		misc/plot-bamstats
+REPLACE_PERL+=		test/test.pl
+REPLACE_PYTHON=		misc/*.py
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../biology/htslib/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/curses.buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/samtools/PLIST b/samtools/PLIST
new file mode 100644
index 0000000000..7b812362b5
--- /dev/null
+++ b/samtools/PLIST
@@ -0,0 +1,24 @@
+@comment $NetBSD: PLIST,v 1.1 2018/05/07 18:37:31 bacon Exp $
+bin/ace2sam
+bin/blast2sam.pl
+bin/bowtie2sam.pl
+bin/export2sam.pl
+bin/interpolate_sam.pl
+bin/maq2sam-long
+bin/maq2sam-short
+bin/md5fa
+bin/md5sum-lite
+bin/novo2sam.pl
+bin/plot-bamstats
+bin/psl2sam.pl
+bin/sam2vcf.pl
+bin/samtools
+bin/samtools.pl
+bin/seq_cache_populate.pl
+bin/soap2sam.pl
+bin/varfilter.py
+bin/wgsim
+bin/wgsim_eval.pl
+bin/zoom2sam.pl
+man/man1/samtools.1
+man/man1/wgsim.1
diff --git a/samtools/TODO b/samtools/TODO
new file mode 100644
index 0000000000..f1db9acbd6
--- /dev/null
+++ b/samtools/TODO
@@ -0,0 +1,3 @@
+Figure out who removed zlib/bl3 in biology/samtools
+
+Address vulnerability
diff --git a/samtools/distinfo b/samtools/distinfo
new file mode 100644
index 0000000000..5100c09cb1
--- /dev/null
+++ b/samtools/distinfo
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.2 2018/11/06 10:49:41 adam Exp $
+
+SHA1 (samtools-1.9.tar.bz2) = 267191dc2f5d24eb0b22c0094138270ed5384241
+RMD160 (samtools-1.9.tar.bz2) = b7f49e1bdd569f63ec53330f43df7e5566ba8a16
+SHA512 (samtools-1.9.tar.bz2) = 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f
+Size (samtools-1.9.tar.bz2) = 4440405 bytes