biology/pbbam: PacBio BAM C++ library, with SWIG bindings

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15154

4 files changed, 181 insertions, 0 deletions

diff --git a/biology/pbbam/Makefile b/biology/pbbam/Makefile
new file mode 100644
index 000000000000..6e492411d4ca
--- /dev/null
+++ b/biology/pbbam/Makefile
@@ -0,0 +1,35 @@
+# $FreeBSD$
+
+PORTNAME=	pbbam
+DISTVERSION=	g20180416
+CATEGORIES=	biology
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	PacBio BAM C++ library, with SWIG bindings
+
+LICENSE=	BSD3CLAUSE
+LICENSE_FILE=	${WRKSRC}/LICENSE.txt
+
+BUILD_DEPENDS=	boost-libs>=1.60.0:devel/boost-libs
+LIB_DEPENDS=	libhts.so:biology/htslib \
+		libboost_regex.so:devel/boost-libs
+
+USES=		cmake pkgconfig
+USE_GITHUB=	yes
+GH_ACCOUNT=	PacificBiosciences
+GH_TAGNAME=	c6b8113adb5104948879e9ff69f739121f12a09f
+
+# Disable tests for now.  Bound to bundled googletest.
+CMAKE_ARGS+=	-DHTSLIB_INCLUDE_DIRS:STRING=${LOCALBASE}/include/htslib \
+		-DHTSLIB_LIBRARIES:STRING="-L${LOCALBASE}/lib -lhts" \
+		-DPacBioBAM_build_tests:BOOL=OFF \
+		-DPacBioBAM_build_docs:BOOL=OFF
+
+do-install:
+	${INSTALL_PROGRAM} ${BUILD_WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin
+	${INSTALL_DATA} ${BUILD_WRKSRC}/lib/* ${STAGEDIR}${PREFIX}/lib
+	cd ${WRKSRC}/include && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include
+	${MV} ${STAGEDIR}${PREFIX}/include/meson.build \
+		${STAGEDIR}${PREFIX}/include/pbbam
+
+.include <bsd.port.mk>
diff --git a/biology/pbbam/distinfo b/biology/pbbam/distinfo
new file mode 100644
index 000000000000..2b1ef8a2a92a
--- /dev/null
+++ b/biology/pbbam/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1524331626
+SHA256 (PacificBiosciences-pbbam-g20180416-c6b8113adb5104948879e9ff69f739121f12a09f_GH0.tar.gz) = f7ede42417110db4fcc3fbc4b837911a0e2242e541a88c8ac34b4c26b4e5aad4
+SIZE (PacificBiosciences-pbbam-g20180416-c6b8113adb5104948879e9ff69f739121f12a09f_GH0.tar.gz) = 8105156
diff --git a/biology/pbbam/pkg-descr b/biology/pbbam/pkg-descr
new file mode 100644
index 000000000000..e69614ed4778
--- /dev/null
+++ b/biology/pbbam/pkg-descr
@@ -0,0 +1,11 @@
+As of the 3.0 release of SMRTanalysis, PacBio is embracing the industry
+standard BAM format for (both aligned and unaligned) basecall data files. We
+have also formulated a BAM companion file format (bam.pbi) enabling fast access
+to a richer set of per-read information as well as compatibility for software
+built around the legacy cmp.h5 format.
+
+The pbbam software package provides components to create, query, & edit PacBio
+BAM files and associated indices. These components include a core C++ library,
+bindings for additional languages, and command-line utilities.
+
+WWW: https://github.com/PacificBiosciences/pbbam
diff --git a/biology/pbbam/pkg-plist b/biology/pbbam/pkg-plist
new file mode 100644
index 000000000000..6b9679b00240
--- /dev/null
+++ b/biology/pbbam/pkg-plist
@@ -0,0 +1,132 @@
+bin/bam2sam
+bin/pbbamify
+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/BamRecord.h
+include/pbbam/BamRecordBuilder.h
+include/pbbam/BamRecordImpl.h
+include/pbbam/BamRecordTag.h
+include/pbbam/BamRecordView.h
+include/pbbam/BamTagCodec.h
+include/pbbam/BamWriter.h
+include/pbbam/BarcodeQuery.h
+include/pbbam/Cigar.h
+include/pbbam/CigarOperation.h
+include/pbbam/ClipType.h
+include/pbbam/Compare.h
+include/pbbam/CompositeBamReader.h
+include/pbbam/CompositeFastaReader.h
+include/pbbam/Config.h
+include/pbbam/DataSet.h
+include/pbbam/DataSetTypes.h
+include/pbbam/DataSetXsd.h
+include/pbbam/EntireFileQuery.h
+include/pbbam/FastaReader.h
+include/pbbam/FastaSequence.h
+include/pbbam/FastaSequenceQuery.h
+include/pbbam/FastqReader.h
+include/pbbam/FastqSequence.h
+include/pbbam/FrameEncodingType.h
+include/pbbam/Frames.h
+include/pbbam/GenomicInterval.h
+include/pbbam/GenomicIntervalQuery.h
+include/pbbam/IRecordWriter.h
+include/pbbam/IndexedBamWriter.h
+include/pbbam/IndexedFastaReader.h
+include/pbbam/Interval.h
+include/pbbam/LocalContextFlags.h
+include/pbbam/MD5.h
+include/pbbam/MakeUnique.h
+include/pbbam/MoveAppend.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/PbiRawData.h
+include/pbbam/Position.h
+include/pbbam/ProgramInfo.h
+include/pbbam/PulseBehavior.h
+include/pbbam/PulseExclusionReason.h
+include/pbbam/QNameQuery.h
+include/pbbam/QualityValue.h
+include/pbbam/QualityValues.h
+include/pbbam/ReadAccuracyQuery.h
+include/pbbam/ReadGroupInfo.h
+include/pbbam/RecordType.h
+include/pbbam/SamTagCodec.h
+include/pbbam/SamWriter.h
+include/pbbam/SequenceInfo.h
+include/pbbam/Strand.h
+include/pbbam/StringUtilities.h
+include/pbbam/SubreadLengthQuery.h
+include/pbbam/Tag.h
+include/pbbam/TagCollection.h
+include/pbbam/Unused.h
+include/pbbam/Validator.h
+include/pbbam/ZmwGroupQuery.h
+include/pbbam/ZmwQuery.h
+include/pbbam/ZmwType.h
+include/pbbam/ZmwTypeMap.h
+include/pbbam/exception/BundleChemistryMappingException.h
+include/pbbam/exception/InvalidSequencingChemistryException.h
+include/pbbam/exception/ValidationException.h
+include/pbbam/internal/Accuracy.inl
+include/pbbam/internal/BamHeader.inl
+include/pbbam/internal/BamRecord.inl
+include/pbbam/internal/BamRecordBuilder.inl
+include/pbbam/internal/BamRecordImpl.inl
+include/pbbam/internal/BamRecordView.inl
+include/pbbam/internal/Cigar.inl
+include/pbbam/internal/CigarOperation.inl
+include/pbbam/internal/Compare.inl
+include/pbbam/internal/CompositeBamReader.inl
+include/pbbam/internal/CompositeFastaReader.inl
+include/pbbam/internal/DataSet.inl
+include/pbbam/internal/DataSetBaseTypes.h
+include/pbbam/internal/DataSetBaseTypes.inl
+include/pbbam/internal/DataSetElement.h
+include/pbbam/internal/DataSetElement.inl
+include/pbbam/internal/DataSetListElement.h
+include/pbbam/internal/DataSetListElement.inl
+include/pbbam/internal/DataSetTypes.inl
+include/pbbam/internal/FastaSequence.inl
+include/pbbam/internal/FastqSequence.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/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/meson.build
+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
+lib/libpbbam.a