Current status

bamtools API and toolkit for handling BAM files

2.5.1_2 biology =0 2.5.1_2Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2018-03-28 13:26:48

Last Update: 2020-06-30 18:46:18

SVN Revision: 540909

License: MIT

Description:

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. WWW: https://github.com/pezmaster31/bamtools

SVNWeb : Homepage

pkg-plist: as obtained via: make generate-plist

Expand this list (31 items)

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1. @ldconfig
2. /usr/local/share/licenses/bamtools-2.5.1_2/catalog.mk
3. /usr/local/share/licenses/bamtools-2.5.1_2/LICENSE
4. /usr/local/share/licenses/bamtools-2.5.1_2/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/shared/bamtools_global.h
26. lib/libbamtools.so
27. lib/libbamtools.so.2.5.1
28. libdata/pkgconfig/bamtools-1.pc
29. @owner
30. @group
31. @mode

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Dependency lines:

• For RUN/BUILD depends:
  • bamtools>0:biology/bamtools

• For LIB depends:
  • libbamtools.so:biology/bamtools

To install the port: cd /usr/ports/biology/bamtools/ && make install clean

To add the package: pkg install bamtools

PKGNAME: bamtools

Flavors: there is no flavor information for this port.

distinfo:

TIMESTAMP = 1520126058 SHA256 (pezmaster31-bamtools-v2.5.1_GH0.tar.gz) = 4abd76cbe1ca89d51abc26bf43a92359e5677f34a8258b901a01f38c897873fc SIZE (pezmaster31-bamtools-v2.5.1_GH0.tar.gz) = 549750

Packages: (move your mouse over the cells for more information)

bamtools

ABI	latest	quarterly
FreeBSD:11:aarch64	2.5.1	2.5.1_2
FreeBSD:11:amd64	2.5.1_2	2.5.1_2
FreeBSD:11:armv6	-	2.5.1_2
FreeBSD:11:i386	2.5.1_2	2.5.1_2
FreeBSD:11:mips	-	-
FreeBSD:11:mips64	-	-
FreeBSD:12:aarch64	2.5.1	2.5.1_2
FreeBSD:12:amd64	2.5.1_2	2.5.1_2
FreeBSD:12:armv6	2.5.1	2.5.1_2
FreeBSD:12:armv7	2.5.1	2.5.1_2
FreeBSD:12:i386	2.5.1_2	2.5.1_2
FreeBSD:12:mips	-	-
FreeBSD:12:mips64	-	-
FreeBSD:12:powerpc64	-	2.5.1_2
FreeBSD:13:aarch64	2.5.1_2	2.5.1_2
FreeBSD:13:amd64	2.5.1_2	2.5.1_2
FreeBSD:13:armv6	2.5.1_2	2.5.1_2
FreeBSD:13:armv7	2.5.1_2	2.5.1_2
FreeBSD:13:i386	2.5.1_2	2.5.1_2
FreeBSD:13:mips	-	-
FreeBSD:13:mips64	-	-
FreeBSD:13:powerpc64	2.5.1_2	2.5.1_2
FreeBSD:14:aarch64	2.5.1_2	-
FreeBSD:14:amd64	2.5.1_2	-
FreeBSD:14:armv6	2.5.1_2	-
FreeBSD:14:armv7	2.5.1_2	-
FreeBSD:14:i386	2.5.1_2	-
FreeBSD:14:mips	-	-
FreeBSD:14:mips64	-	-
FreeBSD:14:powerpc64	2.5.1_2	-

 

Dependencies

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:

1. cmake : devel/cmake
2. ninja : devel/ninja

Library dependencies:

1. libjsoncpp.so : devel/jsoncpp

This port is required by:

for Run

1. biology/ddocent

Configuration Options

No options to configure

USES:

cmake

Master Sites:

Expand this list (1 items)

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1. https://codeload.github.com/pezmaster31/bamtools/tar.gz/v2.5.1?dummy=/

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Bump devel/jsoncpp consumers after r540853.

Reported by:	Kevin Oberman <rkoberman@gmail.com>

devel/jsoncpp: Update 1.8.1 -> 1.9.2

PR:		229677
Differential Revision:	D22905

Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine

biology/bamtools: API and toolkit for handling BAM files

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D14877

12 vulnerabilities affecting 72 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2021-03-28 22:40:29