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Port details
pbbam PacBio BAM C++ library, with SWIG bindings
0.18.0_3 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.18.0Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-23 16:08:32
Last Update: 2019-08-19 16:35:28
SVN Revision: 509290
License: BSD3CLAUSE
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (153 items)
  1. /usr/local/share/licenses/pbbam-0.18.0_3/catalog.mk
  2. /usr/local/share/licenses/pbbam-0.18.0_3/LICENSE
  3. /usr/local/share/licenses/pbbam-0.18.0_3/BSD3CLAUSE
  4. bin/bam2sam
  5. bin/pbbamify
  6. bin/pbindex
  7. bin/pbindexdump
  8. bin/pbmerge
  9. include/pbbam/Accuracy.h
  10. include/pbbam/AlignmentPrinter.h
  11. include/pbbam/BaiIndexedBamReader.h
  12. include/pbbam/BamFile.h
  13. include/pbbam/BamHeader.h
  14. include/pbbam/BamReader.h
  15. include/pbbam/BamRecord.h
  16. include/pbbam/BamRecordBuilder.h
  17. include/pbbam/BamRecordImpl.h
  18. include/pbbam/BamRecordTag.h
  19. include/pbbam/BamRecordView.h
  20. include/pbbam/BamTagCodec.h
  21. include/pbbam/BamWriter.h
  22. include/pbbam/BarcodeQuery.h
  23. include/pbbam/Cigar.h
  24. include/pbbam/CigarOperation.h
  25. include/pbbam/ClipType.h
  26. include/pbbam/Compare.h
  27. include/pbbam/CompositeBamReader.h
  28. include/pbbam/CompositeFastaReader.h
  29. include/pbbam/Config.h
  30. include/pbbam/DataSet.h
  31. include/pbbam/DataSetTypes.h
  32. include/pbbam/DataSetXsd.h
  33. include/pbbam/EntireFileQuery.h
  34. include/pbbam/FastaReader.h
  35. include/pbbam/FastaSequence.h
  36. include/pbbam/FastaSequenceQuery.h
  37. include/pbbam/FastqReader.h
  38. include/pbbam/FastqSequence.h
  39. include/pbbam/FrameEncodingType.h
  40. include/pbbam/Frames.h
  41. include/pbbam/GenomicInterval.h
  42. include/pbbam/GenomicIntervalQuery.h
  43. include/pbbam/IRecordWriter.h
  44. include/pbbam/IndexedBamWriter.h
  45. include/pbbam/IndexedFastaReader.h
  46. include/pbbam/Interval.h
  47. include/pbbam/LocalContextFlags.h
  48. include/pbbam/MD5.h
  49. include/pbbam/MakeUnique.h
  50. include/pbbam/MoveAppend.h
  51. include/pbbam/Orientation.h
  52. include/pbbam/PbiBasicTypes.h
  53. include/pbbam/PbiBuilder.h
  54. include/pbbam/PbiFile.h
  55. include/pbbam/PbiFilter.h
  56. include/pbbam/PbiFilterQuery.h
  57. include/pbbam/PbiFilterTypes.h
  58. include/pbbam/PbiIndexedBamReader.h
  59. include/pbbam/PbiRawData.h
  60. include/pbbam/Position.h
  61. include/pbbam/ProgramInfo.h
  62. include/pbbam/PulseBehavior.h
  63. include/pbbam/PulseExclusionReason.h
  64. include/pbbam/QNameQuery.h
  65. include/pbbam/QualityValue.h
  66. include/pbbam/QualityValues.h
  67. include/pbbam/ReadAccuracyQuery.h
  68. include/pbbam/ReadGroupInfo.h
  69. include/pbbam/RecordType.h
  70. include/pbbam/SamTagCodec.h
  71. include/pbbam/SamWriter.h
  72. include/pbbam/SequenceInfo.h
  73. include/pbbam/Strand.h
  74. include/pbbam/StringUtilities.h
  75. include/pbbam/SubreadLengthQuery.h
  76. include/pbbam/Tag.h
  77. include/pbbam/TagCollection.h
  78. include/pbbam/Unused.h
  79. include/pbbam/Validator.h
  80. include/pbbam/ZmwGroupQuery.h
  81. include/pbbam/ZmwQuery.h
  82. include/pbbam/ZmwType.h
  83. include/pbbam/ZmwTypeMap.h
  84. include/pbbam/exception/BundleChemistryMappingException.h
  85. include/pbbam/exception/InvalidSequencingChemistryException.h
  86. include/pbbam/exception/ValidationException.h
  87. include/pbbam/internal/Accuracy.inl
  88. include/pbbam/internal/BamHeader.inl
  89. include/pbbam/internal/BamRecord.inl
  90. include/pbbam/internal/BamRecordBuilder.inl
  91. include/pbbam/internal/BamRecordImpl.inl
  92. include/pbbam/internal/BamRecordView.inl
  93. include/pbbam/internal/Cigar.inl
  94. include/pbbam/internal/CigarOperation.inl
  95. include/pbbam/internal/Compare.inl
  96. include/pbbam/internal/CompositeBamReader.inl
  97. include/pbbam/internal/CompositeFastaReader.inl
  98. include/pbbam/internal/DataSet.inl
  99. include/pbbam/internal/DataSetBaseTypes.h
  100. include/pbbam/internal/DataSetBaseTypes.inl
  101. include/pbbam/internal/DataSetElement.h
  102. include/pbbam/internal/DataSetElement.inl
  103. include/pbbam/internal/DataSetListElement.h
  104. include/pbbam/internal/DataSetListElement.inl
  105. include/pbbam/internal/DataSetTypes.inl
  106. include/pbbam/internal/FastaSequence.inl
  107. include/pbbam/internal/FastqSequence.inl
  108. include/pbbam/internal/Frames.inl
  109. include/pbbam/internal/GenomicInterval.inl
  110. include/pbbam/internal/Interval.inl
  111. include/pbbam/internal/PbiBasicTypes.inl
  112. include/pbbam/internal/PbiFilter.inl
  113. include/pbbam/internal/PbiFilterTypes.inl
  114. include/pbbam/internal/PbiRawData.inl
  115. include/pbbam/internal/ProgramInfo.inl
  116. include/pbbam/internal/QualityValue.inl
  117. include/pbbam/internal/QualityValues.inl
  118. include/pbbam/internal/QueryBase.h
  119. include/pbbam/internal/QueryBase.inl
  120. include/pbbam/internal/ReadGroupInfo.inl
  121. include/pbbam/internal/SequenceInfo.inl
  122. include/pbbam/internal/Tag.inl
  123. include/pbbam/internal/Validator.inl
  124. include/pbbam/vcf/VcfFile.h
  125. include/pbbam/vcf/VcfFormat.h
  126. include/pbbam/vcf/VcfHeader.h
  127. include/pbbam/vcf/VcfHeaderTypes.h
  128. include/pbbam/vcf/VcfQuery.h
  129. include/pbbam/vcf/VcfReader.h
  130. include/pbbam/vcf/VcfSort.h
  131. include/pbbam/vcf/VcfVariant.h
  132. include/pbbam/vcf/VcfWriter.h
  133. include/pbbam/vcf/internal/VcfFile.inl
  134. include/pbbam/vcf/internal/VcfHeader.inl
  135. include/pbbam/vcf/internal/VcfHeaderTypes.inl
  136. include/pbbam/vcf/internal/VcfVariant.inl
  137. include/pbbam/virtual/VirtualPolymeraseBamRecord.h
  138. include/pbbam/virtual/VirtualPolymeraseCompositeReader.h
  139. include/pbbam/virtual/VirtualPolymeraseReader.h
  140. include/pbbam/virtual/VirtualRegion.h
  141. include/pbbam/virtual/VirtualRegionType.h
  142. include/pbbam/virtual/VirtualRegionTypeMap.h
  143. include/pbbam/virtual/VirtualZmwBamRecord.h
  144. include/pbbam/virtual/WhitelistedZmwReadStitcher.h
  145. include/pbbam/virtual/ZmwReadStitcher.h
  146. include/pbbam/virtual/ZmwWhitelistVirtualReader.h
  147. lib/libpbbam.so
  148. lib/libpbbam.so.0
  149. lib/libpbbam.so.0.18
  150. lib/libpbbam.so.0.18.0
  151. libdata/pkgconfig/pbbam.pc
  152. @postexec /usr/sbin/service ldconfig restart > /dev/null
  153. @postunexec /usr/sbin/service ldconfig restart > /dev/null
Collapse this list.
Dependency lines:
  • pbbam>0:biology/pbbam
To install the port: cd /usr/ports/biology/pbbam/ && make install clean
To add the package: pkg install pbbam
PKGNAME: pbbam
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. meson : devel/meson
  2. ninja : devel/ninja
  3. pkgconf>=1.3.0_1 : devel/pkgconf
  4. python3.6 : lang/python36
Runtime dependencies:
  1. python3.6 : lang/python36
Library dependencies:
  1. libhts.so : biology/htslib
  2. libboost_regex.so : devel/boost-libs
This port is required by:
for Libraries
  1. biology/unanimity

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/PacificBiosciences/pbbam/tar.gz/0.18.0?dummy=/

Number of commits found: 9

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
19 Aug 2019 15:35:28
Original commit files touched by this commit  0.18.0_3
Revision:509290
jbeich search for other commits by this committer
devel/boost-*: update to 1.71.0

Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774
26 Jul 2019 20:46:57
Original commit files touched by this commit  0.18.0_2
Revision:507372
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
12 Apr 2019 06:36:31
Original commit files touched by this commit  0.18.0_1
Revision:498698
jbeich search for other commits by this committer
devel/boost-*: update to 1.70.0

Changes:	http://www.boost.org/users/history/version_1_70_0.html
PR:		235956
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D19303
19 Feb 2019 23:03:41
Original commit files touched by this commit  0.18.0
Revision:493399
jwb search for other commits by this committer
biology/pbbam: Upgrade to 0.18.0 release

In preparation for unanimity upgrade
12 Dec 2018 01:35:36
Original commit files touched by this commit  g20180416_3
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
12 Dec 2018 00:15:50
Original commit files touched by this commit  g20180416_2
Revision:487266
jbeich search for other commits by this committer
devel/boost-*: update to 1.69.0

Changes:	http://www.boost.org/users/history/version_1_69_0.html
PR:		232525
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D17645
18 Sep 2018 08:14:23
Original commit files touched by this commit  g20180416_1
Revision:479990
linimon search for other commits by this committer
More precisely specify USES=compiler to fix build on gcc-based
platforms such as powerpc64.

Tested on powerpc64, amd64.

Approved by:	portmgr (tier-2 blanket)
09 Aug 2018 06:58:31
Original commit files touched by this commit  g20180416_1
Revision:476723
jbeich search for other commits by this committer
devel/boost-*: update to 1.68.0

- Switch to C++14 for libboost_system to support C++14 consumers

Changes:	http://www.boost.org/users/history/version_1_68_0.html
PR:		229569
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D16165
23 Apr 2018 16:08:21
Original commit files touched by this commit  g20180416
Revision:468100
jwb search for other commits by this committer
biology/pbbam: PacBio BAM C++ library, with SWIG bindings

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

Number of commits found: 9

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