Importing htslib-1.3

[i3enedek <pkgsrc_git%i3enedek.neomailbox.net@localhost>]

Module Name:	pkgsrc-wip
Committed By:	i3enedek <pkgsrc_git%i3enedek.neomailbox.net@localhost>
Pushed By:	i3enedek
Date:		Sat Mar 19 01:35:51 2016 +0000
Changeset:	40ded0b7359b21d52ed1c1ee88c95cb429979057

Added Files:
	htslib/DESCR
	htslib/Makefile
	htslib/PLIST
	htslib/buildlink3.mk
	htslib/distinfo

Log Message:
Importing htslib-1.3

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=40ded0b7359b21d52ed1c1ee88c95cb429979057

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

diffstat:
 htslib/DESCR         | 12 ++++++++++++
 htslib/Makefile      | 19 +++++++++++++++++++
 htslib/PLIST         | 36 ++++++++++++++++++++++++++++++++++++
 htslib/buildlink3.mk | 12 ++++++++++++
 htslib/distinfo      |  6 ++++++
 5 files changed, 85 insertions(+)

diffs:
diff --git a/htslib/DESCR b/htslib/DESCR
new file mode 100644
index 0000000..220164d
--- /dev/null
+++ b/htslib/DESCR
@@ -0,0 +1,12 @@
+HTSlib is an implementation of a unified C library for accessing common file
+formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data,
+and is the core library used by samtools and bcftools.
+HTSlib only depends on zlib.
+It is known to be compatible with gcc, g++ and clang.
+
+HTSlib implements a generalized BAM index, with file extension .csi
+(coordinate-sorted index). The HTSlib file reader first looks for the new
+index and then for the old if the new index is absent.
+
+This project also includes the popular tabix indexer, which indexes
+both .tbi and .csi formats, and the bgzip compression utility.
diff --git a/htslib/Makefile b/htslib/Makefile
new file mode 100644
index 0000000..29466d6
--- /dev/null
+++ b/htslib/Makefile
@@ -0,0 +1,19 @@
+# $NetBSD$
+
+DISTNAME=	htslib-1.3
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
+EXTRACT_SUFX=	.tar.bz2
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/samtools/htslib/releases/download/1.3/
+COMMENT=	C library for high-throughput sequencing data formats
+LICENSE=	mit
+
+GNU_CONFIGURE=	yes
+USE_TOOLS+=	pkg-config gmake
+
+#PKGCONFIG_OVERRIDE+=	htslib.pc.in
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/htslib/PLIST b/htslib/PLIST
new file mode 100644
index 0000000..a040045
--- /dev/null
+++ b/htslib/PLIST
@@ -0,0 +1,36 @@
+@comment $NetBSD$
+bin/bgzip
+bin/htsfile
+bin/tabix
+include/htslib/bgzf.h
+include/htslib/cram.h
+include/htslib/faidx.h
+include/htslib/hfile.h
+include/htslib/hts.h
+include/htslib/hts_defs.h
+include/htslib/kbitset.h
+include/htslib/kfunc.h
+include/htslib/khash.h
+include/htslib/khash_str2int.h
+include/htslib/klist.h
+include/htslib/knetfile.h
+include/htslib/kseq.h
+include/htslib/ksort.h
+include/htslib/kstring.h
+include/htslib/regidx.h
+include/htslib/sam.h
+include/htslib/synced_bcf_reader.h
+include/htslib/tbx.h
+include/htslib/vcf.h
+include/htslib/vcf_sweep.h
+include/htslib/vcfutils.h
+lib/libhts.a
+lib/libhts.so
+lib/libhts.so.1
+lib/libhts.so.${PKGVERSION}
+lib/pkgconfig/htslib.pc
+man/man1/htsfile.1
+man/man1/tabix.1
+man/man5/faidx.5
+man/man5/sam.5
+man/man5/vcf.5
diff --git a/htslib/buildlink3.mk b/htslib/buildlink3.mk
new file mode 100644
index 0000000..1d945e5
--- /dev/null
+++ b/htslib/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	htslib
+
+.if !defined(HTSLIB_BUILDLINK3_MK)
+HTSLIB_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.htslib+=	htslib>=1.3
+BUILDLINK_PKGSRCDIR.htslib?=	../../wip/htslib
+.endif	# HTSLIB_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-htslib
diff --git a/htslib/distinfo b/htslib/distinfo
new file mode 100644
index 0000000..f2cc5a4
--- /dev/null
+++ b/htslib/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (htslib-1.3.tar.bz2) = 917981547952ad02e6041a6032e0cc18896b92ec
+RMD160 (htslib-1.3.tar.bz2) = 0947a319f2f9263a100902e9e065c07d79dc6be3
+SHA512 (htslib-1.3.tar.bz2) = 1a96fd22632b4a593596645b3a40aa59aaaaa9f342f97ec8c1807fe4058576420ba2c6279594d00bfc67db93aa858bd63bf3e2cf1a63e79605791c6f8aef097c
+Size (htslib-1.3.tar.bz2) = 952864 bytes