samtools: Testing upgrade to 1.9

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Sep 19 09:23:54 2018 -0500
Changeset:	e7ecaa256d540834fe5f4fba36248ee22ddc23a7

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

Log Message:
samtools: Testing upgrade to 1.9

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e7ecaa256d540834fe5f4fba36248ee22ddc23a7

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 | 25 +++++++++++++++++++++++++
 samtools/PLIST    | 24 ++++++++++++++++++++++++
 samtools/distinfo |  6 ++++++
 5 files changed, 59 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 859203adfa..f0447efafc 100644
--- a/Makefile
+++ b/Makefile
@@ -4178,6 +4178,7 @@ SUBDIR+=	sais-demo-data
 SUBDIR+=	salmon
 SUBDIR+=	samhain
 SUBDIR+=	samtools0119
+SUBDIR+=	samtools
 SUBDIR+=	sara
 SUBDIR+=	sarf
 SUBDIR+=	sawfish
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..998e260fac
--- /dev/null
+++ b/samtools/Makefile
@@ -0,0 +1,25 @@
+# $NetBSD: Makefile,v 1.1 2018/05/07 18:37:31 bacon Exp $
+
+DISTNAME=	samtools-1.9
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
+GITHUB_TAG=	${PKGVERSION_NOREV}
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	http://www.htslib.org/
+COMMENT=	Tools for manipulating next-generation sequencing data
+LICENSE=	mit
+
+USE_TOOLS+=	autoconf automake autoreconf gmake perl:run
+GNU_CONFIGURE=	yes
+REPLACE_PERL=	misc/*.pl misc/plot-bamstats test/test.pl
+REPLACE_PYTHON=	misc/*.py
+
+pre-configure:
+	cd ${WRKSRC} && autoreconf
+
+.include "../../mk/curses.buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../wip/htslib/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/samtools/PLIST b/samtools/PLIST
new file mode 100644
index 0000000000..5ab65fe32e
--- /dev/null
+++ b/samtools/PLIST
@@ -0,0 +1,24 @@
+@comment $NetBSD$
+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/distinfo b/samtools/distinfo
new file mode 100644
index 0000000000..50ed513e70
--- /dev/null
+++ b/samtools/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (samtools-1.9.tar.gz) = d5e163f7d7b232f99ac36d7749d5786b77af59d9
+RMD160 (samtools-1.9.tar.gz) = 8c1ce9afbd2865bc659c80f093839afb6db105ae
+SHA512 (samtools-1.9.tar.gz) = 4c50a365987fd5fa4ddaaa5056587e6b7ccaaacb67dc37880fe242f015a5e1acb94eb8b631184f91a5f4434b84bbf9805acbaee75be1dd9edb76b594fcff0c91
+Size (samtools-1.9.tar.gz) = 4098992 bytes