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Port details
htslib C library for high-throughput sequencing data formats
1.6 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
Maintainer: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 14 Dec 2014 22:35:26
Also Listed In: devel
License: BSD3CLAUSE MIT
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.

WWW: http://www.htslib.org/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (45 items)
  1. /usr/local/share/licenses/htslib-1.6/catalog.mk
  2. /usr/local/share/licenses/htslib-1.6/LICENSE
  3. /usr/local/share/licenses/htslib-1.6/BSD3CLAUSE
  4. /usr/local/share/licenses/htslib-1.6/MIT
  5. bin/bgzip
  6. bin/htsfile
  7. bin/tabix
  8. include/htslib/bgzf.h
  9. include/htslib/cram.h
  10. include/htslib/faidx.h
  11. include/htslib/hfile.h
  12. include/htslib/hts.h
  13. include/htslib/hts_defs.h
  14. include/htslib/hts_endian.h
  15. include/htslib/hts_log.h
  16. include/htslib/hts_os.h
  17. include/htslib/kbitset.h
  18. include/htslib/kfunc.h
  19. include/htslib/khash.h
  20. include/htslib/khash_str2int.h
  21. include/htslib/klist.h
  22. include/htslib/knetfile.h
  23. include/htslib/kseq.h
  24. include/htslib/ksort.h
  25. include/htslib/kstring.h
  26. include/htslib/regidx.h
  27. include/htslib/sam.h
  28. include/htslib/synced_bcf_reader.h
  29. include/htslib/tbx.h
  30. include/htslib/thread_pool.h
  31. include/htslib/vcf.h
  32. include/htslib/vcf_sweep.h
  33. include/htslib/vcfutils.h
  34. lib/libhts.a
  35. lib/libhts.so
  36. lib/libhts.so.1.6
  37. lib/libhts.so.2
  38. libdata/pkgconfig/htslib.pc
  39. man/man1/htsfile.1.gz
  40. man/man1/tabix.1.gz
  41. man/man5/faidx.5.gz
  42. man/man5/sam.5.gz
  43. man/man5/vcf.5.gz
  44. @postexec /sbin/ldconfig -m /usr/local/lib
  45. @postunexec /sbin/ldconfig -R
  46. Collapse this list.

To install the port: cd /usr/ports/biology/htslib/ && make install clean
To add the package: pkg install htslib

PKGNAME: htslib

distinfo:

TIMESTAMP = 1508301522
SHA256 (samtools-htslib-1.6_GH0.tar.gz) = 4215c9153c27603cbaaf542f2ec128c5e839380d6df6edd4dbf67955170740c6
SIZE (samtools-htslib-1.6_GH0.tar.gz) = 1155672


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

Build dependencies:
  1. autoconf-2.69 : devel/autoconf
  2. autoheader-2.69 : devel/autoconf
  3. autoreconf-2.69 : devel/autoconf
  4. aclocal-1.15 : devel/automake
  5. automake-1.15 : devel/automake
  6. gmake : devel/gmake
Library dependencies:
  1. libcurl.so : ftp/curl

This port is required by:

for Build for Libraries * - 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
===> The following configuration options are available for htslib-1.6:
     CURL=on: Use libcurl for network file access (HTTPS and S3 support).
===> Use 'make config' to modify these settings

USES:
autoreconf gmake pathfix perl5 shebangfix

Master Sites:
  1. https://codeload.github.com/samtools/htslib/tar.gz/1.6?dummy=/

Number of commits found: 9

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
25 Oct 2017 10:19:50
Original commit files touched by this commit  1.6
Revision:452840
pizzamig search for other commits by this committer
biology/htslib biology/bcftools biology/samtools: Update to 1.6

PR:		223094
Submitted by:	mzaki@niid.go.jp
Approved by:	cartwright@asu.edu (maintainer)
Approved by:	olivier (mentor)
Differential Revision:	https://reviews.freebsd.org/D12768
21 Oct 2016 15:21:13
Original commit files touched by this commit  1.3.1
Revision:424427
mat search for other commits by this committer
Use USES=pathfix where applicable.

PR:		213195
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D8093
26 May 2016 20:28:55
Original commit files touched by this commit  1.3.1
Revision:415914
pi search for other commits by this committer
biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1

Changes:
  https://sourceforge.net/p/samtools/mailman/message/35033807/

PR:		209653
Submitted by:	cartwright@asu.edu (maintainer)
01 Apr 2016 13:29:17
Original commit files touched by this commit  1.3
Revision:412344
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
29 Dec 2015 15:05:44
Original commit files touched by this commit  1.3
Revision:404749
marino search for other commits by this committer
biology/htslib: Replace FreeBSD-specific fix with a generic one

This port will not build if ENOTRECOVERABLE is not defined, period.
It's not necessary to check OPSYS and version, just apply the fallback
definition if it's not defined.  This unbreaks DragonFly after last
commit.
25 Dec 2015 01:31:09
Original commit files touched by this commit  1.3
Revision:404398
junovitch search for other commits by this committer
biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3

- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
  version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's

PR:		205524
PR:		205525
PR:		205526
Submitted by:	cartwright@asu.edu (maintainer)
06 May 2015 15:16:54
Original commit files touched by this commit  1.2.1
Revision:385521
mat search for other commits by this committer
Update ports in the [bcd]* categories to not use GH_COMMIT.

With minor cleanups to make things simpler.

With hat:	portmgr
Sponsored by:	Absolight
06 Mar 2015 12:45:23
Original commit files touched by this commit  1.2.1
Revision:380596
robak search for other commits by this committer
biology/htslib: update 1.1 -> 1.2.1

PR:		198291
Submitted by:	Reed Cartwright <cartwright@asu.edu>
14 Dec 2014 22:35:08
Original commit files touched by this commit  1.1
Revision:374729
pawel search for other commits by this committer
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.

WWW: http://www.htslib.org/

PR:		195591
Submitted by:	Reed A. Cartwright <cartwright@asu.edu>

Number of commits found: 9

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