biology/htslib: import htslib-1.8

HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.

5 files changed, 94 insertions, 0 deletions

diff --git a/biology/htslib/DESCR b/biology/htslib/DESCR
new file mode 100644
index 00000000000..050ad06ba93
--- /dev/null
+++ b/biology/htslib/DESCR
@@ -0,0 +1,3 @@
+HTSlib is an implementation of a unified C library for accessing common file
+formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
+data. It is the core library used by samtools and bcftools.
diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile
new file mode 100644
index 00000000000..19525f4b265
--- /dev/null
+++ b/biology/htslib/Makefile
@@ -0,0 +1,31 @@
+# $NetBSD: Makefile,v 1.1 2018/04/30 16:51:54 bacon Exp $
+
+DISTNAME=	htslib-1.8
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
+GITHUB_PROJECT=	htslib
+GITHUB_TAG=	${PKGVERSION_NOREV}
+
+MAINTAINER=	bacon@NetBSD.org
+HOMEPAGE=	http://www.htslib.org/
+COMMENT=	C library for high-throughput sequencing data formats
+LICENSE=	mit
+
+USE_TOOLS+=	autoconf automake autoreconf gmake perl
+GNU_CONFIGURE=	yes
+REPLACE_PERL=	test/compare_sam.pl test/test.pl
+
+SUBST_CLASSES+=		version
+SUBST_STAGE.version=	post-patch
+SUBST_SED.version=	-e "s|m4_esyscmd_s(\[make print-version\])|[${PKGVERSION_NOREV}]|"
+SUBST_FILES.version=	${WRKSRC}/configure.ac
+
+PKGCONFIG_OVERRIDE=	htslib.pc.in
+
+pre-configure:
+	cd ${WRKSRC} && autoreconf
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../archivers/xz/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/htslib/PLIST b/biology/htslib/PLIST
new file mode 100644
index 00000000000..ca2d06e3dda
--- /dev/null
+++ b/biology/htslib/PLIST
@@ -0,0 +1,41 @@
+@comment $NetBSD: PLIST,v 1.1 2018/04/30 16:51:54 bacon Exp $
+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/hts_endian.h
+include/htslib/hts_log.h
+include/htslib/hts_os.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/thread_pool.h
+include/htslib/vcf.h
+include/htslib/vcf_sweep.h
+include/htslib/vcfutils.h
+lib/libhts.a
+lib/libhts.so
+lib/libhts.so.${PKGVERSION}
+lib/libhts.so.2
+lib/pkgconfig/htslib.pc
+man/man1/bgzip.1
+man/man1/htsfile.1
+man/man1/tabix.1
+man/man5/faidx.5
+man/man5/sam.5
+man/man5/vcf.5
diff --git a/biology/htslib/buildlink3.mk b/biology/htslib/buildlink3.mk
new file mode 100644
index 00000000000..8862f6018d0
--- /dev/null
+++ b/biology/htslib/buildlink3.mk
@@ -0,0 +1,13 @@
+# $NetBSD: buildlink3.mk,v 1.1 2018/04/30 16:51:54 bacon Exp $
+
+BUILDLINK_TREE+=	htslib
+
+.if !defined(HTSLIB_BUILDLINK3_MK)
+HTSLIB_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.htslib+=	htslib>=1.8
+BUILDLINK_PKGSRCDIR.htslib?=	../../wip/htslib
+
+.endif	# HTSLIB_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-htslib
diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo
new file mode 100644
index 00000000000..43a9456bbdc
--- /dev/null
+++ b/biology/htslib/distinfo
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2018/04/30 16:51:54 bacon Exp $
+
+SHA1 (htslib-1.8.tar.gz) = bc9dd2ca08de99b0b30bb7f5d64bfa0e8c3d35fd
+RMD160 (htslib-1.8.tar.gz) = 400ee0a4994c01e314394bd6a2dceedaa93ec7af
+SHA512 (htslib-1.8.tar.gz) = 888c815d5b202a624cfc99dfe4f795825defd4dcd2420153314096c8fe79532e0a21e0be6bd3b5a4f86dfa1e7c4524271b3f960ab871812abe5a1961d05d568c
+Size (htslib-1.8.tar.gz) = 1262465 bytes