notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
This referral link gives you 10% off a Fastmail.com account and gives me a discount on my Fastmail account.

Get notified when packages are built

A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

FInally, under Watch Lists, click on ABI Package Subscriptions to select your ABI (e.g. FreeBSD:14:amd64) & package set (latest/quarterly) combinatio for a given watch list. This is what FreshPorts will look for.

Port details
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.

Number of commits found: 20

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.18.0_8
06 Jan 2023 01:25:09
commit hash: 843737c597a8e98d41dd666cfe89a00479716fe5commit hash: 843737c597a8e98d41dd666cfe89a00479716fe5commit hash: 843737c597a8e98d41dd666cfe89a00479716fe5commit hash: 843737c597a8e98d41dd666cfe89a00479716fe5 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/pbbam: Bump PORTREVISION for biology/htslib update
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
0.18.0_7
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.18.0_7
12 Aug 2022 14:46:53
commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
*/*: bump all consumers after recent boost upgrade
0.18.0_6
22 May 2022 20:17:16
commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
devel/boost-all: bump all library consumers after boost upgrade

PR:	246106
0.18.0_5
16 Oct 2021 09:51:39
commit hash: 4460cf727a7788c9ce21f3344ce5745e5cd9fc4acommit hash: 4460cf727a7788c9ce21f3344ce5745e5cd9fc4acommit hash: 4460cf727a7788c9ce21f3344ce5745e5cd9fc4acommit hash: 4460cf727a7788c9ce21f3344ce5745e5cd9fc4a files touched by this commit
Jimmy Olgeni (olgeni) search for other commits by this committer
*: fix tab vs. space issues, and comments according to the guide.
0.18.0_5
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
0.18.0_5
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
0.18.0_5
03 Aug 2020 17:40:04
Revision:544090Original commit files touched by this commit
jwb search for other commits by this committer
biology/htslib: Upgrade to 1.10.2

Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags

Bump PORTREVISION on dependents that don't require additional patching

PR:             248089
0.18.0_4
11 Dec 2019 17:53:49
Revision:519824Original commit files touched by this commit
jbeich search for other commits by this committer
devel/boost-*: update to 1.72.0

Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136
0.18.0_3
24 Nov 2019 15:53:01
Revision:518334Original commit files touched by this commit
jwb search for other commits by this committer
biology/unanimity and dependencies: Flag as no longer open source

PacBio now provides unanimity only as a binary package through bioconda.
See https://github.com/PacificBiosciences/ccs.
0.18.0_3
19 Aug 2019 15:35:28
Revision:509290Original commit files touched by this commit
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
0.18.0_2
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
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
0.18.0_1
12 Apr 2019 06:36:31
Revision:498698Original commit files touched by this commit
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
0.18.0
19 Feb 2019 23:03:41
Revision:493399Original commit files touched by this commit
jwb search for other commits by this committer
biology/pbbam: Upgrade to 0.18.0 release

In preparation for unanimity upgrade
g20180416_3
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
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
g20180416_2
12 Dec 2018 00:15:50
Revision:487266Original commit files touched by this commit
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
g20180416_1
18 Sep 2018 08:14:23
Revision:479990Original commit files touched by this commit
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)
g20180416_1
09 Aug 2018 06:58:31
Revision:476723Original commit files touched by this commit
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
g20180416
23 Apr 2018 16:08:21
Revision:468100Original commit files touched by this commit
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: 20