'Add pbbam: PacBio BAM C++ library, with SWIG bindings'

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: 'Add pbbam: PacBio BAM C++ library, with SWIG bindings'
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Sat, 17 Sep 2016 14:05:22 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Sat Sep 17 09:05:22 2016 -0500
Changeset:	050e8f893b3e82c1b85675248a958fe92b759bb0

Modified Files:
	Makefile
Added Files:
	pbbam/DESCR
	pbbam/Makefile
	pbbam/PLIST
	pbbam/TODO
	pbbam/buildlink3.mk
	pbbam/distinfo
	pbbam/patches/patch-src_MD5.cpp

Log Message:
'Add pbbam: 	PacBio BAM C++ library, with SWIG bindings'

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=050e8f893b3e82c1b85675248a958fe92b759bb0

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

diffstat:
 Makefile                        |   1 +
 pbbam/DESCR                     |   1 +
 pbbam/Makefile                  |  51 ++++++++++++++++++
 pbbam/PLIST                     | 111 ++++++++++++++++++++++++++++++++++++++++
 pbbam/TODO                      |   1 +
 pbbam/buildlink3.mk             |  24 +++++++++
 pbbam/distinfo                  |   7 +++
 pbbam/patches/patch-src_MD5.cpp |  15 ++++++
 8 files changed, 211 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 969067b..82aa838 100644
--- a/Makefile
+++ b/Makefile
@@ -2391,6 +2391,7 @@ SUBDIR+=	pasmo
 SUBDIR+=	passepartout
 SUBDIR+=	paxmirabilis
 SUBDIR+=	paxtest
+SUBDIR+=	pbbam
 SUBDIR+=	pbbuttonsd
 SUBDIR+=	pbcopper
 SUBDIR+=	pcmanfm-qt
diff --git a/pbbam/DESCR b/pbbam/DESCR
new file mode 100644
index 0000000..53da43f
--- /dev/null
+++ b/pbbam/DESCR
@@ -0,0 +1 @@
+PacBio BAM C++ library, with SWIG bindings
diff --git a/pbbam/Makefile b/pbbam/Makefile
new file mode 100644
index 0000000..11e7630
--- /dev/null
+++ b/pbbam/Makefile
@@ -0,0 +1,51 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Mon Sep 12 17:24:02 CDT 2016               #
+###########################################################
+
+DISTNAME=	pbbam-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=PacificBiosciences/}
+GITHUB_PROJECT=	pbbam
+GITHUB_TAG=	e46654e0e0b816230c16f4a6132c1feff633a62a
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	https://github.com/PacificBiosciences/pbbam
+COMMENT=	PacBio BAM C++ library, with SWIG bindings
+LICENSE=	modified-bsd
+
+MAKE_JOBS_SAFE=	yes
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	pax
+USE_CMAKE=	yes
+# FIXME: Disable tests for now.  Bound to bundled googletest.
+CMAKE_ARGS=	-DHTSLIB_INCLUDE_DIRS:STRING=${PREFIX}/include/htslib \
+		-DHTSLIB_LIBRARIES:STRING="-L${PREFIX}/lib" \
+		-DPacBioBAM_build_tests:BOOL=OFF \
+		-DPacBioBAM_build_docs:BOOL=OFF
+GCC_REQD=	4.9	# pbcopper requires 4.9 due to use of json
+
+CXXFLAGS+=	-O2
+
+WRKSRC=		${WRKDIR}/pbbam-${GITHUB_TAG}
+
+PORTVERSION=	2016.09.13
+
+INSTALLATION_DIRS=	bin lib ${PKGMANDIR}/man1 share/doc share/examples
+
+MAKE_FLAGS+=	VERBOSE=1
+# FIXME: Shouldn't buildlink provide this?
+LDFLAGS+=	-L${PREFIX}/lib -lhts -lssl
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${DESTDIR}${PREFIX}/bin
+	${INSTALL_DATA} ${WRKSRC}/lib/* ${DESTDIR}${PREFIX}/lib
+	cd ${WRKSRC}/include && pax -rw * ${DESTDIR}${PREFIX}/include
+
+.include "../../devel/boost-libs/buildlink3.mk"
+.include "../../wip/htslib/buildlink3.mk"
+.include "../../security/openssl/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/pbbam/PLIST b/pbbam/PLIST
new file mode 100644
index 0000000..795cead
--- /dev/null
+++ b/pbbam/PLIST
@@ -0,0 +1,111 @@
+@comment $NetBSD$
+bin/bam2sam
+bin/pbindex
+bin/pbindexdump
+bin/pbmerge
+include/pbbam/Accuracy.h
+include/pbbam/AlignmentPrinter.h
+include/pbbam/BaiIndexedBamReader.h
+include/pbbam/BamFile.h
+include/pbbam/BamHeader.h
+include/pbbam/BamReader.h
+include/pbbam/BamRecordBuilder.h
+include/pbbam/BamRecord.h
+include/pbbam/BamRecordImpl.h
+include/pbbam/BamTagCodec.h
+include/pbbam/BamWriter.h
+include/pbbam/BarcodeQuery.h
+include/pbbam/Cigar.h
+include/pbbam/CigarOperation.h
+include/pbbam/Compare.h
+include/pbbam/CompositeBamReader.h
+include/pbbam/Config.h
+include/pbbam/DataSet.h
+include/pbbam/DataSetTypes.h
+include/pbbam/DataSetXsd.h
+include/pbbam/EntireFileQuery.h
+include/pbbam/exception/InvalidSequencingChemistryException.h
+include/pbbam/exception/ValidationException.h
+include/pbbam/Frames.h
+include/pbbam/GenomicInterval.h
+include/pbbam/GenomicIntervalQuery.h
+include/pbbam/IndexedFastaReader.h
+include/pbbam/internal/Accuracy.inl
+include/pbbam/internal/BamHeader.inl
+include/pbbam/internal/BamRecordBuilder.inl
+include/pbbam/internal/BamRecordImpl.inl
+include/pbbam/internal/BamRecord.inl
+include/pbbam/internal/Cigar.inl
+include/pbbam/internal/CigarOperation.inl
+include/pbbam/internal/Compare.inl
+include/pbbam/internal/CompositeBamReader.inl
+include/pbbam/internal/DataSetBaseTypes.h
+include/pbbam/internal/DataSetBaseTypes.inl
+include/pbbam/internal/DataSetElement.h
+include/pbbam/internal/DataSetElement.inl
+include/pbbam/internal/DataSet.inl
+include/pbbam/internal/DataSetListElement.h
+include/pbbam/internal/DataSetListElement.inl
+include/pbbam/internal/DataSetTypes.inl
+include/pbbam/internal/Frames.inl
+include/pbbam/internal/GenomicInterval.inl
+include/pbbam/internal/Interval.inl
+include/pbbam/internal/PbiBasicTypes.inl
+include/pbbam/internal/PbiFilter.inl
+include/pbbam/internal/PbiFilterTypes.inl
+include/pbbam/internal/PbiIndex.inl
+include/pbbam/internal/PbiLookupData.inl
+include/pbbam/internal/PbiRawData.inl
+include/pbbam/internal/ProgramInfo.inl
+include/pbbam/internal/QualityValue.inl
+include/pbbam/internal/QualityValues.inl
+include/pbbam/internal/QueryBase.h
+include/pbbam/internal/QueryBase.inl
+include/pbbam/internal/ReadGroupInfo.inl
+include/pbbam/internal/SequenceInfo.inl
+include/pbbam/internal/Tag.inl
+include/pbbam/internal/Validator.inl
+include/pbbam/Interval.h
+include/pbbam/LocalContextFlags.h
+include/pbbam/MD5.h
+include/pbbam/Orientation.h
+include/pbbam/PbiBasicTypes.h
+include/pbbam/PbiBuilder.h
+include/pbbam/PbiFile.h
+include/pbbam/PbiFilter.h
+include/pbbam/PbiFilterQuery.h
+include/pbbam/PbiFilterTypes.h
+include/pbbam/PbiIndexedBamReader.h
+include/pbbam/PbiIndex.h
+include/pbbam/PbiLookupData.h
+include/pbbam/PbiRawData.h
+include/pbbam/Position.h
+include/pbbam/ProgramInfo.h
+include/pbbam/QNameQuery.h
+include/pbbam/QualityValue.h
+include/pbbam/QualityValues.h
+include/pbbam/ReadAccuracyQuery.h
+include/pbbam/ReadGroupInfo.h
+include/pbbam/SamTagCodec.h
+include/pbbam/SequenceInfo.h
+include/pbbam/Strand.h
+include/pbbam/SubreadLengthQuery.h
+include/pbbam/TagCollection.h
+include/pbbam/Tag.h
+include/pbbam/UnmappedReadsQuery.h
+include/pbbam/Validator.h
+include/pbbam/virtual/VirtualPolymeraseBamRecord.h
+include/pbbam/virtual/VirtualPolymeraseCompositeReader.h
+include/pbbam/virtual/VirtualPolymeraseReader.h
+include/pbbam/virtual/VirtualRegion.h
+include/pbbam/virtual/VirtualRegionType.h
+include/pbbam/virtual/VirtualRegionTypeMap.h
+include/pbbam/virtual/VirtualZmwBamRecord.h
+include/pbbam/virtual/WhitelistedZmwReadStitcher.h
+include/pbbam/virtual/ZmwReadStitcher.h
+include/pbbam/virtual/ZmwWhitelistVirtualReader.h
+include/pbbam/ZmwGroupQuery.h
+include/pbbam/ZmwQuery.h
+include/pbbam/ZmwType.h
+include/pbbam/ZmwTypeMap.h
+lib/libpbbam.a
diff --git a/pbbam/TODO b/pbbam/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/pbbam/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/pbbam/buildlink3.mk b/pbbam/buildlink3.mk
new file mode 100644
index 0000000..5585c9e
--- /dev/null
+++ b/pbbam/buildlink3.mk
@@ -0,0 +1,24 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	pbbam
+
+.if !defined(PBBAM_BUILDLINK3_MK)
+PBBAM_BUILDLINK3_MK:=
+
+BUILDLINK_DEPMETHOD.pbbam?=	build
+
+BUILDLINK_API_DEPENDS.pbbam+=	pbbam>=2016.09.13
+BUILDLINK_PKGSRCDIR.pbbam?=	../../wip/pbbam
+
+# XXX
+# XXX Uncomment and keep only the buildlink3 lines below which are directly
+# XXX needed for dependencies to compile, link, and run.  If this package
+# XXX provides a wrappered API or otherwise does not expose the APIs of the
+# XXX buildlink3 lines below to dependencies, remove them.
+# XXX
+#.include "../../devel/boost-libs/buildlink3.mk"
+#.include "../../wip/htslib/buildlink3.mk"
+#.include "../../security/openssl/buildlink3.mk"
+.endif	# PBBAM_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-pbbam
diff --git a/pbbam/distinfo b/pbbam/distinfo
new file mode 100644
index 0000000..306ef80
--- /dev/null
+++ b/pbbam/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (pbbam-2016.09.13-e46654e0e0b816230c16f4a6132c1feff633a62a.tar.gz) = 022c6160969505cdc495a9573c3f9effc5c52152
+RMD160 (pbbam-2016.09.13-e46654e0e0b816230c16f4a6132c1feff633a62a.tar.gz) = 010dd296d08a46ffc5aa74681338c5b6a90a6442
+SHA512 (pbbam-2016.09.13-e46654e0e0b816230c16f4a6132c1feff633a62a.tar.gz) = 2c7ea6187ebb057951e70773905ce6dc971cbb59864c861e55b51d45253fe5c4b7c1547344eba171f69ab7fd71beb7dd4b74c4947054c7befe23f702f2805f84
+Size (pbbam-2016.09.13-e46654e0e0b816230c16f4a6132c1feff633a62a.tar.gz) = 5394101 bytes
+SHA1 (patch-src_MD5.cpp) = cc7f845a08678b87075142e92f479cc5ac876037
diff --git a/pbbam/patches/patch-src_MD5.cpp b/pbbam/patches/patch-src_MD5.cpp
new file mode 100644
index 0000000..1891a6f
--- /dev/null
+++ b/pbbam/patches/patch-src_MD5.cpp
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Use external ssl
+
+--- src/MD5.cpp.orig	2016-07-12 16:00:45 UTC
++++ src/MD5.cpp
+@@ -40,7 +40,7 @@
+ // Author: Brett Bowman
+ 
+ #include "pbbam/MD5.h"
+-#include <cram/md5.h>
++#include <openssl/md5.h>
+ 
+ namespace PacBio {
+ namespace BAM {
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