biology/pbbam: PacBio BAM C++ library, with SWIG bindings
Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15154
This commit is contained in:
Jason W. Bacon
parent
01c8f600d1
commit
96c9c54cd4
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=468100
@ -81,6 +81,7 @@
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SUBDIR += p5-TrimGalore
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SUBDIR += p5-transdecoder
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SUBDIR += paml
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SUBDIR += pbbam
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SUBDIR += pbseqan
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SUBDIR += pear-merger
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SUBDIR += phrap
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35
biology/pbbam/Makefile
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35
biology/pbbam/Makefile
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# $FreeBSD$
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PORTNAME= pbbam
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DISTVERSION= g20180416
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CATEGORIES= biology
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= PacBio BAM C++ library, with SWIG bindings
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LICENSE= BSD3CLAUSE
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LICENSE_FILE= ${WRKSRC}/LICENSE.txt
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BUILD_DEPENDS= boost-libs>=1.60.0:devel/boost-libs
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LIB_DEPENDS= libhts.so:biology/htslib \
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libboost_regex.so:devel/boost-libs
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USES= cmake pkgconfig
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USE_GITHUB= yes
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GH_ACCOUNT= PacificBiosciences
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GH_TAGNAME= c6b8113adb5104948879e9ff69f739121f12a09f
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# Disable tests for now. Bound to bundled googletest.
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CMAKE_ARGS+= -DHTSLIB_INCLUDE_DIRS:STRING=${LOCALBASE}/include/htslib \
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-DHTSLIB_LIBRARIES:STRING="-L${LOCALBASE}/lib -lhts" \
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-DPacBioBAM_build_tests:BOOL=OFF \
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-DPacBioBAM_build_docs:BOOL=OFF
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do-install:
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${INSTALL_PROGRAM} ${BUILD_WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin
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${INSTALL_DATA} ${BUILD_WRKSRC}/lib/* ${STAGEDIR}${PREFIX}/lib
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cd ${WRKSRC}/include && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include
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${MV} ${STAGEDIR}${PREFIX}/include/meson.build \
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${STAGEDIR}${PREFIX}/include/pbbam
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.include <bsd.port.mk>
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3
biology/pbbam/distinfo
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3
biology/pbbam/distinfo
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@ -0,0 +1,3 @@
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TIMESTAMP = 1524331626
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SHA256 (PacificBiosciences-pbbam-g20180416-c6b8113adb5104948879e9ff69f739121f12a09f_GH0.tar.gz) = f7ede42417110db4fcc3fbc4b837911a0e2242e541a88c8ac34b4c26b4e5aad4
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SIZE (PacificBiosciences-pbbam-g20180416-c6b8113adb5104948879e9ff69f739121f12a09f_GH0.tar.gz) = 8105156
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11
biology/pbbam/pkg-descr
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11
biology/pbbam/pkg-descr
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@ -0,0 +1,11 @@
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As of the 3.0 release of SMRTanalysis, PacBio is embracing the industry
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standard BAM format for (both aligned and unaligned) basecall data files. We
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have also formulated a BAM companion file format (bam.pbi) enabling fast access
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to a richer set of per-read information as well as compatibility for software
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built around the legacy cmp.h5 format.
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The pbbam software package provides components to create, query, & edit PacBio
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BAM files and associated indices. These components include a core C++ library,
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bindings for additional languages, and command-line utilities.
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WWW: https://github.com/PacificBiosciences/pbbam
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132
biology/pbbam/pkg-plist
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132
biology/pbbam/pkg-plist
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@ -0,0 +1,132 @@
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bin/bam2sam
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bin/pbbamify
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bin/pbindex
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bin/pbindexdump
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bin/pbmerge
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include/pbbam/Accuracy.h
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include/pbbam/AlignmentPrinter.h
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include/pbbam/BaiIndexedBamReader.h
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include/pbbam/BamFile.h
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include/pbbam/BamHeader.h
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include/pbbam/BamReader.h
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include/pbbam/BamRecord.h
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include/pbbam/BamRecordBuilder.h
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include/pbbam/BamRecordImpl.h
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include/pbbam/BamRecordTag.h
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include/pbbam/BamRecordView.h
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include/pbbam/BamTagCodec.h
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include/pbbam/BamWriter.h
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include/pbbam/BarcodeQuery.h
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include/pbbam/Cigar.h
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include/pbbam/CigarOperation.h
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include/pbbam/ClipType.h
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include/pbbam/Compare.h
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include/pbbam/CompositeBamReader.h
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include/pbbam/CompositeFastaReader.h
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include/pbbam/Config.h
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include/pbbam/DataSet.h
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include/pbbam/DataSetTypes.h
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include/pbbam/DataSetXsd.h
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include/pbbam/EntireFileQuery.h
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include/pbbam/FastaReader.h
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include/pbbam/FastaSequence.h
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include/pbbam/FastaSequenceQuery.h
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include/pbbam/FastqReader.h
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include/pbbam/FastqSequence.h
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include/pbbam/FrameEncodingType.h
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include/pbbam/Frames.h
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include/pbbam/GenomicInterval.h
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include/pbbam/GenomicIntervalQuery.h
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include/pbbam/IRecordWriter.h
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include/pbbam/IndexedBamWriter.h
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include/pbbam/IndexedFastaReader.h
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include/pbbam/Interval.h
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include/pbbam/LocalContextFlags.h
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include/pbbam/MD5.h
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include/pbbam/MakeUnique.h
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include/pbbam/MoveAppend.h
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include/pbbam/Orientation.h
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include/pbbam/PbiBasicTypes.h
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include/pbbam/PbiBuilder.h
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include/pbbam/PbiFile.h
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include/pbbam/PbiFilter.h
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include/pbbam/PbiFilterQuery.h
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include/pbbam/PbiFilterTypes.h
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include/pbbam/PbiIndexedBamReader.h
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include/pbbam/PbiRawData.h
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include/pbbam/Position.h
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include/pbbam/ProgramInfo.h
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include/pbbam/PulseBehavior.h
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include/pbbam/PulseExclusionReason.h
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include/pbbam/QNameQuery.h
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include/pbbam/QualityValue.h
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include/pbbam/QualityValues.h
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include/pbbam/ReadAccuracyQuery.h
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include/pbbam/ReadGroupInfo.h
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include/pbbam/RecordType.h
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include/pbbam/SamTagCodec.h
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include/pbbam/SamWriter.h
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include/pbbam/SequenceInfo.h
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include/pbbam/Strand.h
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include/pbbam/StringUtilities.h
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include/pbbam/SubreadLengthQuery.h
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include/pbbam/Tag.h
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include/pbbam/TagCollection.h
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include/pbbam/Unused.h
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include/pbbam/Validator.h
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include/pbbam/ZmwGroupQuery.h
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include/pbbam/ZmwQuery.h
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include/pbbam/ZmwType.h
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include/pbbam/ZmwTypeMap.h
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include/pbbam/exception/BundleChemistryMappingException.h
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include/pbbam/exception/InvalidSequencingChemistryException.h
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include/pbbam/exception/ValidationException.h
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include/pbbam/internal/Accuracy.inl
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include/pbbam/internal/BamHeader.inl
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include/pbbam/internal/BamRecord.inl
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include/pbbam/internal/BamRecordBuilder.inl
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include/pbbam/internal/BamRecordImpl.inl
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include/pbbam/internal/BamRecordView.inl
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include/pbbam/internal/Cigar.inl
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include/pbbam/internal/CigarOperation.inl
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include/pbbam/internal/Compare.inl
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include/pbbam/internal/CompositeBamReader.inl
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include/pbbam/internal/CompositeFastaReader.inl
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include/pbbam/internal/DataSet.inl
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include/pbbam/internal/DataSetBaseTypes.h
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include/pbbam/internal/DataSetBaseTypes.inl
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include/pbbam/internal/DataSetElement.h
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include/pbbam/internal/DataSetElement.inl
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include/pbbam/internal/DataSetListElement.h
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include/pbbam/internal/DataSetListElement.inl
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include/pbbam/internal/DataSetTypes.inl
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include/pbbam/internal/FastaSequence.inl
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include/pbbam/internal/FastqSequence.inl
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include/pbbam/internal/Frames.inl
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include/pbbam/internal/GenomicInterval.inl
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include/pbbam/internal/Interval.inl
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include/pbbam/internal/PbiBasicTypes.inl
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include/pbbam/internal/PbiFilter.inl
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include/pbbam/internal/PbiFilterTypes.inl
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include/pbbam/internal/PbiRawData.inl
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include/pbbam/internal/ProgramInfo.inl
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include/pbbam/internal/QualityValue.inl
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include/pbbam/internal/QualityValues.inl
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include/pbbam/internal/QueryBase.h
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include/pbbam/internal/QueryBase.inl
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include/pbbam/internal/ReadGroupInfo.inl
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include/pbbam/internal/SequenceInfo.inl
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include/pbbam/internal/Tag.inl
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include/pbbam/internal/Validator.inl
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include/pbbam/meson.build
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include/pbbam/virtual/VirtualPolymeraseBamRecord.h
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include/pbbam/virtual/VirtualPolymeraseCompositeReader.h
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include/pbbam/virtual/VirtualPolymeraseReader.h
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include/pbbam/virtual/VirtualRegion.h
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include/pbbam/virtual/VirtualRegionType.h
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include/pbbam/virtual/VirtualRegionTypeMap.h
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include/pbbam/virtual/VirtualZmwBamRecord.h
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include/pbbam/virtual/WhitelistedZmwReadStitcher.h
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include/pbbam/virtual/ZmwReadStitcher.h
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include/pbbam/virtual/ZmwWhitelistVirtualReader.h
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lib/libpbbam.a
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