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Port details
iolib General purpose trace file (and Experiment File) reading interface
1.14.9 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: danilo@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Aug 2009 23:34:46
License: BSD3CLAUSE
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/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (120 items)
  1. /usr/local/share/licenses/io_lib-1.14.9/catalog.mk
  2. /usr/local/share/licenses/io_lib-1.14.9/LICENSE
  3. /usr/local/share/licenses/io_lib-1.14.9/BSD3CLAUSE
  4. bin/append_sff
  5. bin/convert_trace
  6. bin/cram_dump
  7. bin/cram_filter
  8. bin/cram_index
  9. bin/cram_size
  10. bin/extract_fastq
  11. bin/extract_qual
  12. bin/extract_seq
  13. bin/get_comment
  14. bin/hash_exp
  15. bin/hash_extract
  16. bin/hash_list
  17. bin/hash_sff
  18. bin/hash_tar
  19. bin/index_tar
  20. bin/io_lib-config
  21. bin/makeSCF
  22. bin/scf_dump
  23. bin/scf_info
  24. bin/scf_update
  25. bin/scram_flagstat
  26. bin/scram_merge
  27. bin/scram_pileup
  28. bin/scram_test
  29. bin/scramble
  30. bin/srf2fasta
  31. bin/srf2fastq
  32. bin/srf_dump_all
  33. bin/srf_extract_hash
  34. bin/srf_extract_linear
  35. bin/srf_filter
  36. bin/srf_index_hash
  37. bin/srf_info
  38. bin/srf_list
  39. bin/trace_dump
  40. bin/ztr_dump
  41. include/io_lib/Read.h
  42. include/io_lib/abi.h
  43. include/io_lib/alf.h
  44. include/io_lib/array.h
  45. include/io_lib/bam.h
  46. include/io_lib/bgzip.h
  47. include/io_lib/binning.h
  48. include/io_lib/compress.h
  49. include/io_lib/compression.h
  50. include/io_lib/cram.h
  51. include/io_lib/cram_codecs.h
  52. include/io_lib/cram_decode.h
  53. include/io_lib/cram_encode.h
  54. include/io_lib/cram_index.h
  55. include/io_lib/cram_io.h
  56. include/io_lib/cram_stats.h
  57. include/io_lib/cram_structs.h
  58. include/io_lib/deflate_interlaced.h
  59. include/io_lib/dstring.h
  60. include/io_lib/error.h
  61. include/io_lib/expFileIO.h
  62. include/io_lib/fpoint.h
  63. include/io_lib/hash_table.h
  64. include/io_lib/io_lib_config.h
  65. include/io_lib/jenkins_lookup3.h
  66. include/io_lib/mFILE.h
  67. include/io_lib/mach-io.h
  68. include/io_lib/md5.h
  69. include/io_lib/misc.h
  70. include/io_lib/open_trace_file.h
  71. include/io_lib/os.h
  72. include/io_lib/plain.h
  73. include/io_lib/pooled_alloc.h
  74. include/io_lib/sam_header.h
  75. include/io_lib/scf.h
  76. include/io_lib/scf_extras.h
  77. include/io_lib/scram.h
  78. include/io_lib/seqIOABI.h
  79. include/io_lib/sff.h
  80. include/io_lib/srf.h
  81. include/io_lib/stdio_hack.h
  82. include/io_lib/string_alloc.h
  83. include/io_lib/tar_format.h
  84. include/io_lib/thread_pool.h
  85. include/io_lib/traceType.h
  86. include/io_lib/translate.h
  87. include/io_lib/vlen.h
  88. include/io_lib/xalloc.h
  89. include/io_lib/zfio.h
  90. include/io_lib/ztr.h
  91. lib/libstaden-read.a
  92. lib/libstaden-read.so
  93. lib/libstaden-read.so.11
  94. lib/libstaden-read.so.11.1.0
  95. man/man1/scramble.1.gz
  96. man/man1/srf2fasta.1.gz
  97. man/man1/srf2fastq.1.gz
  98. man/man1/srf_index_hash.1.gz
  99. man/man1/srf_info.1.gz
  100. man/man1/srf_list.1.gz
  101. man/man3/ExperimentFile.3.gz
  102. man/man3/exp2read.3.gz
  103. man/man3/fread_reading.3.gz
  104. man/man3/fread_scf.3.gz
  105. man/man3/fwrite_reading.3.gz
  106. man/man3/fwrite_scf.3.gz
  107. man/man3/read2exp.3.gz
  108. man/man3/read2scf.3.gz
  109. man/man3/read_allocate.3.gz
  110. man/man3/read_deallocate.3.gz
  111. man/man3/read_reading.3.gz
  112. man/man3/read_scf.3.gz
  113. man/man3/read_scf_header.3.gz
  114. man/man3/scf2read.3.gz
  115. man/man3/write_reading.3.gz
  116. man/man3/write_scf.3.gz
  117. man/man3/write_scf_header.3.gz
  118. man/man4/Read.4.gz
  119. @postexec /sbin/ldconfig -m /usr/local/lib
  120. @postunexec /sbin/ldconfig -R
  121. Collapse this list.

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

PKGNAME: io_lib

distinfo:

TIMESTAMP = 1488270338
SHA256 (jkbonfield-io_lib-io_lib-1-14-9_GH0.tar.gz) = 077044d525e9dd76f94ee83b0ab19cd655b08348cc81bbdaa84e39c622280a4a
SIZE (jkbonfield-io_lib-io_lib-1-14-9_GH0.tar.gz) = 1396092


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. libtoolize : devel/libtool
  7. gmake : devel/gmake
Library dependencies:
  1. libcurl.so : ftp/curl

This port is required by:

for Build for Run * - 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

USES:
autoreconf gmake libtool

Master Sites:
  1. https://codeload.github.com/jkbonfield/io_lib/tar.gz/io_lib-1-14-9?dummy=/

Number of commits found: 36

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
13 May 2017 03:35:51
Original commit files touched by this commit  1.14.9
Revision:440746
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  1.14.9
Revision:435006
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  1.14.9
Revision:434741
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  1.14.8
Revision:414372
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  1.14.7
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
20 Feb 2016 16:05:59
Original commit files touched by this commit  1.14.7
Revision:409251
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  1.14.6
Revision:401113
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  1.14.5
Revision:400926
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  1.14.4
Revision:398730
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  1.14.3
Revision:398397
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  1.14.2
Revision:397395
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  1.14.2
Revision:397111
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  1.14.1
Revision:396842
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  1.14.0
Revision:391830
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  1.13.10
Revision:380435
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  1.13.9
Revision:378185
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  1.13.8
Revision:377013
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  1.13.7
Revision:371237
bapt search for other commits by this committer
Cleanup plist
31 May 2014 18:03:08
Original commit files touched by this commit  1.13.7
Revision:355999
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  1.13.7
Revision:355998
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  1.13.5
Revision:352216
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  1.13.0_1
Revision:351071
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  1.13.0_1
Revision:340411
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  1.13.0_1
Revision:336171
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  1.13.0_1
Revision:327709
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  1.13.0_1
Revision:322783
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  1.13.0
Revision:316940
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: 36

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