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Port details
iolib General purpose trace file (and Experiment File) reading interface
1.14.10 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 1.14.10Version 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: 2009-08-28 23:34:46
Last Update: 2021-05-19 19:56:24
Commit Hash: 809338d
License: BSD3CLAUSE
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (122 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/io_lib-1.14.10/catalog.mk
  3. /usr/local/share/licenses/io_lib-1.14.10/LICENSE
  4. /usr/local/share/licenses/io_lib-1.14.10/BSD3CLAUSE
  5. bin/append_sff
  6. bin/convert_trace
  7. bin/cram_dump
  8. bin/cram_filter
  9. bin/cram_index
  10. bin/cram_size
  11. bin/extract_fastq
  12. bin/extract_qual
  13. bin/extract_seq
  14. bin/get_comment
  15. bin/hash_exp
  16. bin/hash_extract
  17. bin/hash_list
  18. bin/hash_sff
  19. bin/hash_tar
  20. bin/index_tar
  21. bin/io_lib-config
  22. bin/makeSCF
  23. bin/scf_dump
  24. bin/scf_info
  25. bin/scf_update
  26. bin/scram_flagstat
  27. bin/scram_merge
  28. bin/scram_pileup
  29. bin/scram_test
  30. bin/scramble
  31. bin/srf2fasta
  32. bin/srf2fastq
  33. bin/srf_dump_all
  34. bin/srf_extract_hash
  35. bin/srf_extract_linear
  36. bin/srf_filter
  37. bin/srf_index_hash
  38. bin/srf_info
  39. bin/srf_list
  40. bin/trace_dump
  41. bin/ztr_dump
  42. include/io_lib/Read.h
  43. include/io_lib/abi.h
  44. include/io_lib/alf.h
  45. include/io_lib/array.h
  46. include/io_lib/bam.h
  47. include/io_lib/bgzip.h
  48. include/io_lib/binning.h
  49. include/io_lib/compress.h
  50. include/io_lib/compression.h
  51. include/io_lib/cram.h
  52. include/io_lib/cram_codecs.h
  53. include/io_lib/cram_decode.h
  54. include/io_lib/cram_encode.h
  55. include/io_lib/cram_index.h
  56. include/io_lib/cram_io.h
  57. include/io_lib/cram_stats.h
  58. include/io_lib/cram_structs.h
  59. include/io_lib/deflate_interlaced.h
  60. include/io_lib/dstring.h
  61. include/io_lib/error.h
  62. include/io_lib/expFileIO.h
  63. include/io_lib/fpoint.h
  64. include/io_lib/hash_table.h
  65. include/io_lib/io_lib_config.h
  66. include/io_lib/jenkins_lookup3.h
  67. include/io_lib/mFILE.h
  68. include/io_lib/mach-io.h
  69. include/io_lib/md5.h
  70. include/io_lib/misc.h
  71. include/io_lib/open_trace_file.h
  72. include/io_lib/os.h
  73. include/io_lib/plain.h
  74. include/io_lib/pooled_alloc.h
  75. include/io_lib/sam_header.h
  76. include/io_lib/scf.h
  77. include/io_lib/scf_extras.h
  78. include/io_lib/scram.h
  79. include/io_lib/seqIOABI.h
  80. include/io_lib/sff.h
  81. include/io_lib/srf.h
  82. include/io_lib/stdio_hack.h
  83. include/io_lib/string_alloc.h
  84. include/io_lib/tar_format.h
  85. include/io_lib/thread_pool.h
  86. include/io_lib/traceType.h
  87. include/io_lib/translate.h
  88. include/io_lib/vlen.h
  89. include/io_lib/xalloc.h
  90. include/io_lib/zfio.h
  91. include/io_lib/ztr.h
  92. lib/libstaden-read.a
  93. lib/libstaden-read.so
  94. lib/libstaden-read.so.13
  95. lib/libstaden-read.so.13.0.0
  96. man/man1/scramble.1.gz
  97. man/man1/srf2fasta.1.gz
  98. man/man1/srf2fastq.1.gz
  99. man/man1/srf_index_hash.1.gz
  100. man/man1/srf_info.1.gz
  101. man/man1/srf_list.1.gz
  102. man/man3/ExperimentFile.3.gz
  103. man/man3/exp2read.3.gz
  104. man/man3/fread_reading.3.gz
  105. man/man3/fread_scf.3.gz
  106. man/man3/fwrite_reading.3.gz
  107. man/man3/fwrite_scf.3.gz
  108. man/man3/read2exp.3.gz
  109. man/man3/read2scf.3.gz
  110. man/man3/read_allocate.3.gz
  111. man/man3/read_deallocate.3.gz
  112. man/man3/read_reading.3.gz
  113. man/man3/read_scf.3.gz
  114. man/man3/read_scf_header.3.gz
  115. man/man3/scf2read.3.gz
  116. man/man3/write_reading.3.gz
  117. man/man3/write_scf.3.gz
  118. man/man3/write_scf_header.3.gz
  119. man/man4/Read.4.gz
  120. @owner
  121. @group
  122. @mode
Collapse this list.
Dependency lines:
  • For RUN/BUILD depends:
    • io_lib>0:biology/iolib
  • For LIB depends:
    • libstaden-read.so:biology/iolib
To install the port: cd /usr/ports/biology/iolib/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/iolib
  • pkg install io_lib
PKGNAME: io_lib
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
io_lib
ABIlatestquarterly
FreeBSD:11:aarch641.14.91.14.10
FreeBSD:11:amd641.14.101.14.10
FreeBSD:11:armv61.14.81.14.10
FreeBSD:11:i3861.14.101.14.10
FreeBSD:11:mips--
FreeBSD:11:mips641.14.8-
FreeBSD:12:aarch641.14.101.14.10
FreeBSD:12:amd641.14.101.14.10
FreeBSD:12:armv61.14.101.14.10
FreeBSD:12:armv71.14.101.14.10
FreeBSD:12:i3861.14.101.14.10
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-1.14.10
FreeBSD:13:aarch641.14.101.14.10
FreeBSD:13:amd641.14.101.14.10
FreeBSD:13:armv61.14.101.14.10
FreeBSD:13:armv71.14.101.14.10
FreeBSD:13:i3861.14.101.14.10
FreeBSD:13:mips--
FreeBSD:13:mips641.14.101.14.10
FreeBSD:13:powerpc641.14.101.14.10
FreeBSD:14:aarch641.14.10-
FreeBSD:14:amd641.14.10-
FreeBSD:14:armv61.14.10-
FreeBSD:14:armv71.14.10-
FreeBSD:14:i3861.14.10-
FreeBSD:14:mips--
FreeBSD:14:mips641.14.10-
FreeBSD:14:powerpc641.14.10-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. autoconf>=2.69 : devel/autoconf
  3. automake>=1.16.1 : devel/automake
  4. libtoolize : devel/libtool
Library dependencies:
  1. libcurl.so : ftp/curl
This port is required by:
for Build
  1. biology/p5-Bio-SCF
for Run
  1. biology/p5-Bio-SCF

Configuration Options:
Options name:

USES:

Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/jkbonfield/io_lib/tar.gz/io_lib-1-14-10?dummy=/
Collapse this list.

Number of commits found: 43

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
19 May 2021 19:56:24
 files touched by this commit commit hash:809338d451b2d3e438c1fa44fb30184aa18ff3a6  1.14.10
danilo search for other commits by this committer
biology/iolib: Drop maintainership
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  1.14.10
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
01 Apr 2019 19:33:15
Original commit files touched by this commit Revision:497508  1.14.10
danilo search for other commits by this committer
- Fix build in head i386
05 Nov 2018 19:45:23
Original commit files touched by this commit Revision:484210  1.14.10
linimon search for other commits by this committer
Remove the incorrect typedefs to fix build on tier-2.

PR:		232390
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)
05 Nov 2018 19:42:38
Original commit files touched by this commit Revision:484209  1.14.10
linimon search for other commits by this committer
Remove the inccorrect typedefs to fix build on tier-2.

PR:		232390
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)
28 Sep 2018 18:47:50
Original commit files touched by this commit Revision:480878  1.14.10
danilo search for other commits by this committer
- Update to 1-14-10
- Move USES to make portlint happy
02 Jul 2018 00:47:14
Original commit files touched by this commit Revision:473692  1.14.9
linimon search for other commits by this committer
Mark various ports broken on mips64 and, where appropriate, mips.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
13 May 2017 03:35:51
Original commit files touched by this commit Revision:440746  1.14.9
linimon search for other commits by this committer
Mark some ports failing on power64.  In cases where the error message
was a stub, provide a real one.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
28 Feb 2017 08:33:44
Original commit files touched by this commit Revision:435006  1.14.9
mat search for other commits by this committer
Fix USE_GITHUB's GH_TAGNAME usage.

Sponsored by:	Absolight
24 Feb 2017 18:57:57
Original commit files touched by this commit Revision:434741  1.14.9
danilo search for other commits by this committer
- Update to 1.14.9
- Use github
01 May 2016 01:03:48
Original commit files touched by this commit Revision:414372  1.14.8
danilo search for other commits by this committer
- Update to 1.14.8
01 Apr 2016 13:29:17
Original commit files touched by this commit Revision:412344  1.14.7
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
20 Feb 2016 16:05:59
Original commit files touched by this commit Revision:409251  1.14.7
danilo search for other commits by this committer
- Update to 1.14.7
09 Nov 2015 16:02:13
Original commit files touched by this commit Revision:401113  1.14.6
danilo search for other commits by this committer
- Update to 1.14.6
06 Nov 2015 12:03:25
Original commit files touched by this commit Revision:400926  1.14.5
danilo search for other commits by this committer
- Update to 1.14.5
07 Oct 2015 00:26:34
Original commit files touched by this commit Revision:398730  1.14.4
danilo search for other commits by this committer
- Update to 1.14.4
01 Oct 2015 23:28:23
Original commit files touched by this commit Revision:398397  1.14.3
danilo search for other commits by this committer
- Update to 1.14.3
20 Sep 2015 19:59:04
Original commit files touched by this commit Revision:397395  1.14.2
olgeni search for other commits by this committer
Typos, whitespace and capitalization fixes (A-F).
17 Sep 2015 12:54:48
Original commit files touched by this commit Revision:397111  1.14.2
danilo search for other commits by this committer
- Update to 1.14.2
13 Sep 2015 18:05:55
Original commit files touched by this commit Revision:396842  1.14.1
danilo search for other commits by this committer
- Update to 1.14.1
12 Jul 2015 18:25:07
Original commit files touched by this commit Revision:391830  1.14.0
danilo search for other commits by this committer
- Update to 1.14.0
- Use install-strip
04 Mar 2015 13:17:47
Original commit files touched by this commit Revision:380435  1.13.10
danilo search for other commits by this committer
- Update to 1.13.10
30 Jan 2015 21:49:29
Original commit files touched by this commit Revision:378185  1.13.9
danilo search for other commits by this committer
- Update to 1.13.9
14 Jan 2015 13:15:50
Original commit files touched by this commit Revision:377013  1.13.8
danilo search for other commits by this committer
- Update to 1.13.8
20 Oct 2014 07:10:48
Original commit files touched by this commit Revision:371237  1.13.7
bapt search for other commits by this committer
Cleanup plist
31 May 2014 18:03:08
Original commit files touched by this commit Revision:355999  1.13.7
danilo search for other commits by this committer
- I forgot to svn add a new patch
31 May 2014 17:57:07
Original commit files touched by this commit Revision:355998  1.13.7
danilo search for other commits by this committer
- Update from 1.13.5 to 1.13.7
- Add libtool to USES
- Take maintainership
26 Apr 2014 02:35:37
Original commit files touched by this commit Revision:352216  1.13.5
miwi search for other commits by this committer
- Update to version 1.13.5

PR:		188863
Submitted by:	ports fury
12 Apr 2014 07:42:33
Original commit files touched by this commit Revision:351071  1.13.0_1
culot search for other commits by this committer
- Back to the heap, I don't use this port anymore
20 Jan 2014 17:02:11
Original commit files touched by this commit Revision:340411  1.13.0_1
bapt search for other commits by this committer
Support stage
Conver USE_GMAKE
11 Dec 2013 14:43:51
Original commit files touched by this commit Revision:336171  1.13.0_1
bapt search for other commits by this committer
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
20 Sep 2013 15:55:44
Original commit files touched by this commit Revision:327709  1.13.0_1
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
11 Jul 2013 16:26:27
Original commit files touched by this commit Revision:322783  1.13.0_1
sunpoet search for other commits by this committer
- Update to 7.31.0
- Bump PORTREVISION for ftp/curl shlib change
- Add TEST_DEPENDS
- Convert to new options framework
- Adjust options:
  - Add COOKIES
  - Add CYASSL, NSS, POLARSSL, THREADED_RESOLVER, TLS_SRP [1]
  - Add GSSAPI and SPNEGO [2]
  - Remove KERBEROS4
  - Rename LIBIDN to IDN
  - Remove TRACKMEMORY [1]
- Sort option handler
- Add SLAVEDIRS: ftp/curl-hiphop
- Cosmetic change
- Cleanup Makefile header
- While I'm here, fix typo (PORTREVSION) in x11-wm/ede/Makefile

Changes:	http://curl.haxx.se/changes.html
PR:		ports/172325 (-exp run), ports/177369 (based on) [1]
Submitted by:	Hirohisa Yamaguchi <umq@ueo.co.jp> [1], hrs (via email) [2]
Exp run by:	miwi
30 Apr 2013 15:41:49
Original commit files touched by this commit Revision:316940  1.13.0
culot search for other commits by this committer
- Update to 1.13.0
- Improve COMMENT (remove leading article, add missing space)
- Remove unneeded BSD license file
- Trim Makefile's header
- Pet portlint (move LICENSE section earlier, change tab to space in WWW link)

Changes:	http://sourceforge.net/p/staden/news/2013/03/iolib-1130-released/
09 Nov 2011 15:26:04
Original commit files touched by this commit   1.12.5
miwi search for other commits by this committer
- Remove WITH_FBSD10_FIX, is no longer needed
29 Oct 2011 11:10:22
Original commit files touched by this commit   1.12.5
miwi search for other commits by this committer
- Fix build on FreeBSD 10
11 Feb 2011 13:11:45
Original commit files touched by this commit   1.12.5
culot search for other commits by this committer
- Update to 1.12.5

Changes:        http://sourceforge.net/news/?group_id=100316&id=297223
04 Dec 2010 07:34:27
Original commit files touched by this commit   1.12.4
ade search for other commits by this committer
Sync to new bsd.autotools.mk
20 Oct 2010 05:53:20
Original commit files touched by this commit   1.12.4
culot search for other commits by this committer
Update my MAINTAINER address to culot@FreeBSD.org.

Approved by:    sahil@ (mentor)
02 Aug 2010 16:06:38
Original commit files touched by this commit   1.12.4
bapt search for other commits by this committer
Fix typo in maintainer mail address

Submitted by:   Frederic Culot <frederic _at_ culot.org> (maintainer)
Approved by:    jadawin@ (co-mentor)
02 Aug 2010 15:09:22
Original commit files touched by this commit   1.12.4
bapt search for other commits by this committer
- Update to 1.12.4
- Add libcurl as dependency
- Submitter is now maintainer

PR:             ports/149079
Submitted by:   Frederic Coulot <frederic _at_ coulot.org> (maintainer)
Approved by:    jadawin@ (co-mentor)
21 May 2010 06:19:18
Original commit files touched by this commit   1.12.2
wen search for other commits by this committer
- Update to 1.12.2
- Reset maintainer
28 Aug 2009 23:34:20
Original commit files touched by this commit   1.12.1
miwi search for other commits by this committer
Io_lib is a library of file reading and writing code to provide a
general purpose trace file (and Experiment File) reading interface.
The programmer simply calls the (eg) read_reading to create a "Read"
C structure with the data loaded into memory. It has been compiled
and tested on a variety of unix systems, MacOS X and MS Windows.

WWW:    http://staden.sourceforge.net/

PR:             ports/138254
Submitted by:   Wen Heping <wenheping at gmail.com>

Number of commits found: 43