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Port details on branch 2022Q2
pbbam PacBio BAM C++ library, with SWIG bindings
0.18.0_8 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 View this port on Repology. pkg-fallout 0.18.0_8Version of this port present on the latest quarterly branch.
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-23 16:08:32
Last Update: 2023-01-06 01:25:09
Commit Hash: 843737c
License: BSD3CLAUSE
WWW:
https://github.com/PacificBiosciences/pbbam
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (155 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/pbbam-0.18.0_8/catalog.mk
  3. /usr/local/share/licenses/pbbam-0.18.0_8/LICENSE
  4. /usr/local/share/licenses/pbbam-0.18.0_8/BSD3CLAUSE
  5. bin/bam2sam
  6. bin/pbbamify
  7. bin/pbindex
  8. bin/pbindexdump
  9. bin/pbmerge
  10. include/pbbam/Accuracy.h
  11. include/pbbam/AlignmentPrinter.h
  12. include/pbbam/BaiIndexedBamReader.h
  13. include/pbbam/BamFile.h
  14. include/pbbam/BamHeader.h
  15. include/pbbam/BamReader.h
  16. include/pbbam/BamRecord.h
  17. include/pbbam/BamRecordBuilder.h
  18. include/pbbam/BamRecordImpl.h
  19. include/pbbam/BamRecordTag.h
  20. include/pbbam/BamRecordView.h
  21. include/pbbam/BamTagCodec.h
  22. include/pbbam/BamWriter.h
  23. include/pbbam/BarcodeQuery.h
  24. include/pbbam/Cigar.h
  25. include/pbbam/CigarOperation.h
  26. include/pbbam/ClipType.h
  27. include/pbbam/Compare.h
  28. include/pbbam/CompositeBamReader.h
  29. include/pbbam/CompositeFastaReader.h
  30. include/pbbam/Config.h
  31. include/pbbam/DataSet.h
  32. include/pbbam/DataSetTypes.h
  33. include/pbbam/DataSetXsd.h
  34. include/pbbam/EntireFileQuery.h
  35. include/pbbam/FastaReader.h
  36. include/pbbam/FastaSequence.h
  37. include/pbbam/FastaSequenceQuery.h
  38. include/pbbam/FastqReader.h
  39. include/pbbam/FastqSequence.h
  40. include/pbbam/FrameEncodingType.h
  41. include/pbbam/Frames.h
  42. include/pbbam/GenomicInterval.h
  43. include/pbbam/GenomicIntervalQuery.h
  44. include/pbbam/IRecordWriter.h
  45. include/pbbam/IndexedBamWriter.h
  46. include/pbbam/IndexedFastaReader.h
  47. include/pbbam/Interval.h
  48. include/pbbam/LocalContextFlags.h
  49. include/pbbam/MD5.h
  50. include/pbbam/MakeUnique.h
  51. include/pbbam/MoveAppend.h
  52. include/pbbam/Orientation.h
  53. include/pbbam/PbiBasicTypes.h
  54. include/pbbam/PbiBuilder.h
  55. include/pbbam/PbiFile.h
  56. include/pbbam/PbiFilter.h
  57. include/pbbam/PbiFilterQuery.h
  58. include/pbbam/PbiFilterTypes.h
  59. include/pbbam/PbiIndexedBamReader.h
  60. include/pbbam/PbiRawData.h
  61. include/pbbam/Position.h
  62. include/pbbam/ProgramInfo.h
  63. include/pbbam/PulseBehavior.h
  64. include/pbbam/PulseExclusionReason.h
  65. include/pbbam/QNameQuery.h
  66. include/pbbam/QualityValue.h
  67. include/pbbam/QualityValues.h
  68. include/pbbam/ReadAccuracyQuery.h
  69. include/pbbam/ReadGroupInfo.h
  70. include/pbbam/RecordType.h
  71. include/pbbam/SamTagCodec.h
  72. include/pbbam/SamWriter.h
  73. include/pbbam/SequenceInfo.h
  74. include/pbbam/Strand.h
  75. include/pbbam/StringUtilities.h
  76. include/pbbam/SubreadLengthQuery.h
  77. include/pbbam/Tag.h
  78. include/pbbam/TagCollection.h
  79. include/pbbam/Unused.h
  80. include/pbbam/Validator.h
  81. include/pbbam/ZmwGroupQuery.h
  82. include/pbbam/ZmwQuery.h
  83. include/pbbam/ZmwType.h
  84. include/pbbam/ZmwTypeMap.h
  85. include/pbbam/exception/BundleChemistryMappingException.h
  86. include/pbbam/exception/InvalidSequencingChemistryException.h
  87. include/pbbam/exception/ValidationException.h
  88. include/pbbam/internal/Accuracy.inl
  89. include/pbbam/internal/BamHeader.inl
  90. include/pbbam/internal/BamRecord.inl
  91. include/pbbam/internal/BamRecordBuilder.inl
  92. include/pbbam/internal/BamRecordImpl.inl
  93. include/pbbam/internal/BamRecordView.inl
  94. include/pbbam/internal/Cigar.inl
  95. include/pbbam/internal/CigarOperation.inl
  96. include/pbbam/internal/Compare.inl
  97. include/pbbam/internal/CompositeBamReader.inl
  98. include/pbbam/internal/CompositeFastaReader.inl
  99. include/pbbam/internal/DataSet.inl
  100. include/pbbam/internal/DataSetBaseTypes.h
  101. include/pbbam/internal/DataSetBaseTypes.inl
  102. include/pbbam/internal/DataSetElement.h
  103. include/pbbam/internal/DataSetElement.inl
  104. include/pbbam/internal/DataSetListElement.h
  105. include/pbbam/internal/DataSetListElement.inl
  106. include/pbbam/internal/DataSetTypes.inl
  107. include/pbbam/internal/FastaSequence.inl
  108. include/pbbam/internal/FastqSequence.inl
  109. include/pbbam/internal/Frames.inl
  110. include/pbbam/internal/GenomicInterval.inl
  111. include/pbbam/internal/Interval.inl
  112. include/pbbam/internal/PbiBasicTypes.inl
  113. include/pbbam/internal/PbiFilter.inl
  114. include/pbbam/internal/PbiFilterTypes.inl
  115. include/pbbam/internal/PbiRawData.inl
  116. include/pbbam/internal/ProgramInfo.inl
  117. include/pbbam/internal/QualityValue.inl
  118. include/pbbam/internal/QualityValues.inl
  119. include/pbbam/internal/QueryBase.h
  120. include/pbbam/internal/QueryBase.inl
  121. include/pbbam/internal/ReadGroupInfo.inl
  122. include/pbbam/internal/SequenceInfo.inl
  123. include/pbbam/internal/Tag.inl
  124. include/pbbam/internal/Validator.inl
  125. include/pbbam/vcf/VcfFile.h
  126. include/pbbam/vcf/VcfFormat.h
  127. include/pbbam/vcf/VcfHeader.h
  128. include/pbbam/vcf/VcfHeaderTypes.h
  129. include/pbbam/vcf/VcfQuery.h
  130. include/pbbam/vcf/VcfReader.h
  131. include/pbbam/vcf/VcfSort.h
  132. include/pbbam/vcf/VcfVariant.h
  133. include/pbbam/vcf/VcfWriter.h
  134. include/pbbam/vcf/internal/VcfFile.inl
  135. include/pbbam/vcf/internal/VcfHeader.inl
  136. include/pbbam/vcf/internal/VcfHeaderTypes.inl
  137. include/pbbam/vcf/internal/VcfVariant.inl
  138. include/pbbam/virtual/VirtualPolymeraseBamRecord.h
  139. include/pbbam/virtual/VirtualPolymeraseCompositeReader.h
  140. include/pbbam/virtual/VirtualPolymeraseReader.h
  141. include/pbbam/virtual/VirtualRegion.h
  142. include/pbbam/virtual/VirtualRegionType.h
  143. include/pbbam/virtual/VirtualRegionTypeMap.h
  144. include/pbbam/virtual/VirtualZmwBamRecord.h
  145. include/pbbam/virtual/WhitelistedZmwReadStitcher.h
  146. include/pbbam/virtual/ZmwReadStitcher.h
  147. include/pbbam/virtual/ZmwWhitelistVirtualReader.h
  148. lib/libpbbam.so
  149. lib/libpbbam.so.0
  150. lib/libpbbam.so.0.18
  151. lib/libpbbam.so.0.18.0
  152. libdata/pkgconfig/pbbam.pc
  153. @owner
  154. @group
  155. @mode
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, run one of these commands:
  • pkg install biology/pbbam
  • pkg install pbbam
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: pbbam
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1550453627 SHA256 (PacificBiosciences-pbbam-0.18.0_GH0.tar.gz) = 45286e5f7deb7ff629e0643c8a416155915aec7b85d54c60b5cdc07f4d7b234a SIZE (PacificBiosciences-pbbam-0.18.0_GH0.tar.gz) = 8136503

Packages (timestamps in pop-ups are UTC):
pbbam
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.18.0_80.18.0_80.18.0_50.18.0_80.18.0_8-0.18.0_5-
FreeBSD:13:quarterly0.18.0_80.18.0_80.18.0_80.18.0_80.18.0_80.18.0_80.18.0_80.18.0_8
FreeBSD:14:latest0.18.0_80.18.0_80.18.0_80.18.0_80.18.0_80.18.0_8-0.18.0_8
FreeBSD:14:quarterly0.18.0_80.18.0_8-0.18.0_80.18.0_80.18.0_80.18.0_80.18.0_8
FreeBSD:15:latest0.18.0_80.18.0_8n/a0.18.0_8n/a0.18.0_80.18.0_80.18.0_8
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. meson>=0.57.1_1 : devel/meson
  2. ninja : devel/ninja
  3. pkgconf>=1.3.0_1 : devel/pkgconf
  4. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. python3.9 : lang/python39
Library dependencies:
  1. libhts.so : biology/htslib
  2. libboost_regex.so : devel/boost-libs
This port is required by:
for Libraries

Deleted ports which required this port:

Expand this list of 1 deleted port
  1. biology/unanimity*
  2. Collapse this list of deleted ports.
* - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

Configuration Options:
No options to configure
Options name:
biology_pbbam
USES:
compiler:c++14-lang localbase meson pkgconfig python
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/PacificBiosciences/pbbam/tar.gz/0.18.0?dummy=/
Collapse this list.

There are no commits on branch 2022Q2 for this port