BSD Ports

biology/pbbam 0.18.0_14 FreeBSD

PacBio BAM C++ library, with SWIG bindings

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
97a84ef467
License
BSD3CLAUSE
Categories
biology
Package size
629.7 KiB, 2663.3 KiB installed

Description

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.

In the other systems

SystemPortVersion
FreeBSDbiology/pbbam0.18.0_14
DragonFlybiology/pbbam0.18.0_11
HardenedBSDbiology/pbbam0.18.0_14
GhostBSDbiology/pbbam0.18.0_13

Install

Binary package:

pkg install pbbam

From the ports tree:

cd /usr/ports/biology/pbbam/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	pbbam>0:biology/pbbam
LIB_DEPENDS=	libpbbam.so:biology/pbbam

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest0.18.0_140.18.0_140.18.0_8-0.18.0_14
FreeBSD:14:quarterly0.18.0_140.18.0_14n/a-0.18.0_14
FreeBSD:15:latest0.18.0_140.18.0_14n/a-0.18.0_12
FreeBSD:15:quarterly0.18.0_140.18.0_14n/an/an/a
FreeBSD:16:latest0.18.0_140.18.0_14n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Library 2

The full lists below include those, and their dependencies in turn.

Build dependencies 23
Run dependencies 20

No port depends on this one.

Configuration

No options to configure.

USES
compiler:c++14-lang localbase meson pkgconfig python
Service scripts
none

Message after installing

===>   NOTICE:

The pbbam port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

pkg-plist 148
  • 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

The first 100 are listed.

distinfo 1
FileSizeSHA256
PacificBiosciences-pbbam-0.18.0_GH0.tar.gz8.136503e+0645286e5f7deb7ff629e0643c8a416155915aec7b85d54c60b5cdc07f4d7b234a

Commit history 1

DateCommitCreditsLog message
97a84ef467 Dima Panov */*: update boost consumers after boost-1.92