'Add vcflib: C++ library and CLI tools for parsing and manipulating VCF files'

[Jason Bacon <bacon@centosdev.local>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon@centosdev.local>
Pushed By:	outpaddling
Date:		Thu Mar 30 20:22:05 2017 -0500
Changeset:	8528abeec14004021807a53a3265a7c17eeaa608

Modified Files:
	Makefile
Added Files:
	vcflib/DESCR
	vcflib/Makefile
	vcflib/PLIST
	vcflib/TODO
	vcflib/buildlink3.mk
	vcflib/distinfo

Log Message:
'Add vcflib: 	C++ library and CLI tools for parsing and manipulating VCF files'

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8528abeec14004021807a53a3265a7c17eeaa608

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

diffstat:
 Makefile             |  1 +
 vcflib/DESCR         |  1 +
 vcflib/Makefile      | 73 +++++++++++++++++++++++++++++++++++++++++++++++++++
 vcflib/PLIST         | 74 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 vcflib/TODO          |  1 +
 vcflib/buildlink3.mk | 12 +++++++++
 vcflib/distinfo      |  6 +++++
 7 files changed, 168 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index eb43858a92..ee49f341b7 100644
--- a/Makefile
+++ b/Makefile
@@ -4330,6 +4330,7 @@ SUBDIR+=	vamps
 SUBDIR+=	varnish
 SUBDIR+=	varnish4
 SUBDIR+=	vba-m
+SUBDIR+=	vcflib
 SUBDIR+=	vcftools
 SUBDIR+=	vcg
 SUBDIR+=	vcglib
diff --git a/vcflib/DESCR b/vcflib/DESCR
new file mode 100644
index 0000000000..845dbab1b0
--- /dev/null
+++ b/vcflib/DESCR
@@ -0,0 +1 @@
+[description of the port]
diff --git a/vcflib/Makefile b/vcflib/Makefile
new file mode 100644
index 0000000000..4841aacf4d
--- /dev/null
+++ b/vcflib/Makefile
@@ -0,0 +1,73 @@
+# $NetBSD$
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+DISTNAME=	vcflib-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=outpaddling/}
+GITHUB_TAG=	${PORTVERSION}
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	http://example.com
+COMMENT=	C++ library and CLI tools for parsing and manipulating VCF files
+LICENSE=	mit
+
+# Test and change if necessary.
+# MAKE_JOBS_SAFE=	no
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+# FreeBSD's SHEBANG_FILES may include bash, perl, python, etc.
+# I don't know which is which, so you'll have to finish.
+# Add bash, etc. to USE_TOOLS if used below.
+# 
+# REPLACE_SH=	
+# REPLACE_BASH=	
+# REPLACE_CSH=	
+# REPLACE_KSH=	
+# REPLACE_PERL=	
+# REPLACE_PYTHON=	
+
+CXXFLAGS+=	-I${LOCALBASE}/include/smithwaterman \
+ 		-I${LOCALBASE}/include/multichoose \
+ 		-I${LOCALBASE}/include/filevercmp \
+ 		-I${LOCALBASE}/include/fastahack \
+ 		-I${LOCALBASE}/include/intervaltree
+MAKE_FILE=	Makefile.external-libs
+INSTALL_TARGET=		install-strip
+
+# PORTVERSION=	6451cf639cc7d735137218c4b08f597ba9dd6e73
+PORTVERSION=	790904320065e603c6af5b8a32f635134354467c
+DATADIR=	${PREFIX}/share/vcflib
+DOCSDIR=	${PREFIX}/share/doc/vcflib
+
+#SUBST_CLASSES+=         ldflags
+#SUBST_FILES.ldflags=    ${WRKSRC}/Makefile.external-libs
+#SUBST_STAGE.ldflags=    post-patch
+#SUBST_SED.ldflags=      -e "s|LDFLAGS =|LDFLAGS = ${COMPILER_RPATH_FLAG}${PREFIX}/lib|g"
+
+LDFLAGS+=	${COMPILER_RPATH_FLAG}${PREFIX}/lib
+
+#MAKE_FLAGS=	LIB_PATH+=${COMPILER_RPATH_FLAG}${PREFIX}/lib
+
+# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
+.include "../../mk/bsd.prefs.mk"
+
+# GCC disables sse2 by default on i386, but it's required for vcflib
+.if ${MACHINE_ARCH} == i386
+CFLAGS+=	-msse2
+.endif
+
+.include "../../wip/htslib/buildlink3.mk"
+.include "../../wip/tabixpp/buildlink3.mk"
+.include "../../wip/smithwaterman/buildlink3.mk"
+.include "../../wip/fastahack/buildlink3.mk"
+.include "../../wip/filevercmp/buildlink3.mk"
+.include "../../wip/fsom/buildlink3.mk"
+.include "../../wip/multichoose/buildlink3.mk"
+.include "../../wip/intervaltree/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/vcflib/PLIST b/vcflib/PLIST
new file mode 100644
index 0000000000..77094051a8
--- /dev/null
+++ b/vcflib/PLIST
@@ -0,0 +1,74 @@
+@comment $NetBSD$
+bin/vcf2dag
+bin/vcf2fasta
+bin/vcf2tsv
+bin/vcfaddinfo
+bin/vcfafpath
+bin/vcfallelicprimitives
+bin/vcfaltcount
+bin/vcfannotate
+bin/vcfannotategenotypes
+bin/vcfbreakmulti
+bin/vcfcat
+bin/vcfcheck
+bin/vcfclassify
+bin/vcfcleancomplex
+bin/vcfcombine
+bin/vcfcommonsamples
+bin/vcfcountalleles
+bin/vcfcreatemulti
+bin/vcfdistance
+bin/vcfecho
+bin/vcfentropy
+bin/vcfevenregions
+bin/vcffilter
+bin/vcffixup
+bin/vcfflatten
+bin/vcfgeno2alleles
+bin/vcfgeno2haplo
+bin/vcfgenosamplenames
+bin/vcfgenosummarize
+bin/vcfgenotypecompare
+bin/vcfgenotypes
+bin/vcfglbound
+bin/vcfglxgt
+bin/vcfhetcount
+bin/vcfhethomratio
+bin/vcfindex
+bin/vcfinfo2qual
+bin/vcfinfosummarize
+bin/vcfintersect
+bin/vcfkeepgeno
+bin/vcfkeepinfo
+bin/vcfkeepsamples
+bin/vcfleftalign
+bin/vcflength
+bin/vcfnumalt
+bin/vcfoverlay
+bin/vcfparsealts
+bin/vcfprimers
+bin/vcfqual2info
+bin/vcfrandom
+bin/vcfrandomsample
+bin/vcfremap
+bin/vcfremoveaberrantgenotypes
+bin/vcfremovesamples
+bin/vcfroc
+bin/vcfsample2info
+bin/vcfsamplediff
+bin/vcfsamplenames
+bin/vcfsitesummarize
+bin/vcfstats
+bin/vcfstreamsort
+bin/vcfuniq
+bin/vcfuniqalleles
+include/vcflib/BedReader.h
+include/vcflib/convert.h
+include/vcflib/join.h
+include/vcflib/mt19937ar.h
+include/vcflib/split.h
+include/vcflib/ssw_cpp.h
+include/vcflib/ssw.h
+include/vcflib/Variant.h
+lib/libvcflib.a
+lib/libvcflib.so.1
diff --git a/vcflib/TODO b/vcflib/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/vcflib/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/vcflib/buildlink3.mk b/vcflib/buildlink3.mk
new file mode 100644
index 0000000000..d97e74a071
--- /dev/null
+++ b/vcflib/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	vcflib
+
+.if !defined(VCFLIB_BUILDLINK3_MK)
+VCFLIB_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.vcflib+=	vcflib>=790904320065e603c6af5b8a32f635134354467c
+BUILDLINK_PKGSRCDIR.vcflib?=	../../wip/vcflib
+.endif	# VCFLIB_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-vcflib
diff --git a/vcflib/distinfo b/vcflib/distinfo
new file mode 100644
index 0000000000..83aa3c3f2f
--- /dev/null
+++ b/vcflib/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (vcflib-790904320065e603c6af5b8a32f635134354467c-790904320065e603c6af5b8a32f635134354467c.tar.gz) = 18287d02a6fb2303466f53b447dceaba68133151
+RMD160 (vcflib-790904320065e603c6af5b8a32f635134354467c-790904320065e603c6af5b8a32f635134354467c.tar.gz) = 822055de94c9eeb22e261fabcb19a2e43acbc0fb
+SHA512 (vcflib-790904320065e603c6af5b8a32f635134354467c-790904320065e603c6af5b8a32f635134354467c.tar.gz) = 4518e7277d92eabdc5606ac6297b7350af4e287a3dc6d0bf4f63c7ac1fcc41e4585a7d4c264c8783687086765cbb28874dc85df1f6cdc7be9fe788da6c1132a6
+Size (vcflib-790904320065e603c6af5b8a32f635134354467c-790904320065e603c6af5b8a32f635134354467c.tar.gz) = 121633 bytes