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Port details on branch 2026Q3
bamtools API and toolkit for handling BAM files
2.5.3 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 View this port on Repology. pkg-fallout 2.5.3Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-03-28 13:26:48
Last Update: 2025-05-19 21:21:57
Commit Hash: 101f13e
License: MIT
WWW:
https://github.com/pezmaster31/bamtools
Description:
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. BAM is the binary alternative to the sequence alignment/map (SAM) format used for storing genetic sequence data. It uses BGZF block compression implemented on top of the standard gzip file format to provide good compression while allowing efficient random access for indexed queries.
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 (32 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/bamtools-2.5.3/catalog.mk
  3. /usr/local/share/licenses/bamtools-2.5.3/LICENSE
  4. /usr/local/share/licenses/bamtools-2.5.3/MIT
  5. bin/bamtools
  6. include/bamtools/api/BamAlgorithms.h
  7. include/bamtools/api/BamAlignment.h
  8. include/bamtools/api/BamAux.h
  9. include/bamtools/api/BamConstants.h
  10. include/bamtools/api/BamIndex.h
  11. include/bamtools/api/BamMultiReader.h
  12. include/bamtools/api/BamReader.h
  13. include/bamtools/api/BamWriter.h
  14. include/bamtools/api/IBamIODevice.h
  15. include/bamtools/api/SamConstants.h
  16. include/bamtools/api/SamHeader.h
  17. include/bamtools/api/SamProgram.h
  18. include/bamtools/api/SamProgramChain.h
  19. include/bamtools/api/SamReadGroup.h
  20. include/bamtools/api/SamReadGroupDictionary.h
  21. include/bamtools/api/SamSequence.h
  22. include/bamtools/api/SamSequenceDictionary.h
  23. include/bamtools/api/algorithms/Sort.h
  24. include/bamtools/api/api_global.h
  25. include/bamtools/api/bamtools_api_export.h
  26. include/bamtools/shared/bamtools_global.h
  27. lib/libbamtools.so
  28. lib/libbamtools.so.2.5.3
  29. libdata/pkgconfig/bamtools-1.pc
  30. @owner
  31. @group
  32. @mode
Collapse this list.
USE_RC_SUBR (Service Scripts)
  • no SUBR information found for this port
Dependency lines:
  • bamtools>0:biology/bamtools
To install the port:
cd /usr/ports/biology/bamtools/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/bamtools
  • pkg install bamtools
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: bamtools
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1747676701 SHA256 (pezmaster31-bamtools-v2.5.3_GH0.tar.gz) = 7d4e59bac7c03bde488fe43e533692f78b5325a097328785ec31373ffac08344 SIZE (pezmaster31-bamtools-v2.5.3_GH0.tar.gz) = 245648
Packages (timestamps in pop-ups are UTC):
bamtools
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.5.32.5.3n/an/an/an/an/an/a
FreeBSD:13:quarterly2.5.32.5.3n/an/an/an/an/an/a
FreeBSD:14:latest2.5.32.5.32.5.2_12.5.32.5.32.5.2_1-2.5.2_1
FreeBSD:14:quarterly2.5.32.5.3-2.5.32.5.32.5.2_12.5.2_12.5.2_1
FreeBSD:15:latest2.5.32.5.3n/a2.5.3n/an/a2.5.2_12.5.2_1
FreeBSD:15:quarterly2.5.32.5.3n/a-n/an/a--
FreeBSD:16:latest2.5.32.5.3n/a-n/an/a--
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. cmake : devel/cmake-core
  2. ninja : devel/ninja
Library dependencies:
  1. libjsoncpp.so : devel/jsoncpp
This port is required by:
for Libraries
  1. biology/augustus
for Run
  1. biology/biostar-tools
  2. biology/ddocent
Configuration Options:
No options to configure
Options name:
biology_bamtools
USES:
cmake
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/pezmaster31/bamtools/tar.gz/v2.5.3?dummy=/
Collapse this list.

There are no commits on branch 2026Q3 for this port
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