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r573 | lh3lh3 | 2010-05-11 12:08:30 -0400 (Tue, 11 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/Makefile

Added -fPIC

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r572 | lh3lh3 | 2010-05-11 11:59:07 -0400 (Tue, 11 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/perl/MANIFEST

update

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r571 | lh3lh3 | 2010-05-11 11:56:54 -0400 (Tue, 11 May 2010) | 4 lines
Changed paths:
   A /trunk/tabix/example.gtf.gz
   A /trunk/tabix/example.gtf.gz.tbi
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c
   M /trunk/tabix/perl/MANIFEST
   M /trunk/tabix/perl/Tabix.pm
   M /trunk/tabix/perl/Tabix.xs
   A /trunk/tabix/perl/TabixIterator.pm
   A /trunk/tabix/perl/t
   A /trunk/tabix/perl/t/01local.t
   A /trunk/tabix/perl/t/02remote.t
   M /trunk/tabix/tabix.1
   M /trunk/tabix/tabix.h

 * improved C/Perl APIs
 * added test for Perl
 * added an tiny example

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r570 | lh3lh3 | 2010-05-11 01:04:21 -0400 (Tue, 11 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/TabixReader.java

fixed the same issue in java

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r569 | lh3lh3 | 2010-05-11 01:03:24 -0400 (Tue, 11 May 2010) | 3 lines
Changed paths:
   M /trunk/tabix/index.c
   M /trunk/tabix/perl/Tabix.pm
   M /trunk/tabix/perl/Tabix.xs

 * fixed a potential issue in index.c
 * improve perl APIs

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r568 | lh3lh3 | 2010-05-10 23:46:21 -0400 (Mon, 10 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/perl/Tabix.xs

return an array from get_names()

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r567 | lh3lh3 | 2010-05-10 23:38:46 -0400 (Mon, 10 May 2010) | 4 lines
Changed paths:
   M /trunk/tabix/TabixReader.java
   M /trunk/tabix/index.c
   A /trunk/tabix/perl
   A /trunk/tabix/perl/MANIFEST
   A /trunk/tabix/perl/Makefile.PL
   A /trunk/tabix/perl/Tabix.pm
   A /trunk/tabix/perl/Tabix.xs
   A /trunk/tabix/perl/typemap
   M /trunk/tabix/tabix.h

 * added the initial perl binding. The interface needs to be improved.
 * added a new API for perl binding
 * fixed a potential bug in java.

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r565 | lh3lh3 | 2010-05-09 23:24:35 -0400 (Sun, 09 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/main.c

Release tabix-0.1.6

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r564 | lh3lh3 | 2010-05-09 23:01:49 -0400 (Sun, 09 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/index.c

fixed a typo

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r563 | lh3lh3 | 2010-05-09 22:58:26 -0400 (Sun, 09 May 2010) | 2 lines
Changed paths:
   A /trunk/tabix/ChangeLog
   M /trunk/tabix/NEWS
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c
   M /trunk/tabix/tabix.h

If nothing bad happens, this will become 0.1.6

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r562 | lh3lh3 | 2010-05-09 19:43:56 -0400 (Sun, 09 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/index.c

Fixed a bug

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r560 | lh3lh3 | 2010-05-05 10:59:09 -0400 (Wed, 05 May 2010) | 3 lines
Changed paths:
   A /trunk/tabix/NEWS
   M /trunk/tabix/TabixReader.java
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c
   M /trunk/tabix/tabix.1
   M /trunk/tabix/tabix.h

 * Release tabix-0.1.5 (r560)
 * Improve seeking efficiency. Index file needs to be rebuilt.

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r559 | lh3lh3 | 2010-05-04 23:11:42 -0400 (Tue, 04 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/main.c

Release tabix-0.1.4 (r559)

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r558 | lh3lh3 | 2010-05-01 12:48:01 -0400 (Sat, 01 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/TabixReader.java

implement SAM/VCF support; NOT tested yet

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r557 | lh3lh3 | 2010-05-01 00:42:34 -0400 (Sat, 01 May 2010) | 2 lines
Changed paths:
   A /trunk/tabix/TabixReader.java

The Java implementation of tabix.

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r556 | lh3lh3 | 2010-04-30 22:34:07 -0400 (Fri, 30 Apr 2010) | 4 lines
Changed paths:
   M /trunk/tabix/index.c
   M /trunk/tabix/knetfile.c
   M /trunk/tabix/main.c

 * tabix-0.1.3-3 (r556)
 * fixed a small memory leak in knetfile
 * fixed a minor bug for remote downloading

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r555 | lh3lh3 | 2010-04-30 22:15:12 -0400 (Fri, 30 Apr 2010) | 4 lines
Changed paths:
   M /trunk/tabix/Makefile
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c

 * tabix-0.1.3-2 (r555)
 * do not overwrite index file by default
 * a little code cleanup

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r554 | lh3lh3 | 2010-04-30 21:44:31 -0400 (Fri, 30 Apr 2010) | 2 lines
Changed paths:
   M /trunk/tabix/index.c

fixed a potential bug for UCSC-like coordinate

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r553 | lh3lh3 | 2010-04-28 17:43:41 -0400 (Wed, 28 Apr 2010) | 2 lines
Changed paths:
   M /trunk/tabix/tabix.tex

minor clarification to the format spec

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r552 | lh3lh3 | 2010-04-28 16:33:07 -0400 (Wed, 28 Apr 2010) | 3 lines
Changed paths:
   M /trunk/tabix/Makefile
   M /trunk/tabix/bgzip.c
   A /trunk/tabix/tabix.tex

 * added the format specification
 * fixed a typo in bgzip

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r550 | petulda | 2010-04-22 11:03:24 -0400 (Thu, 22 Apr 2010) | 1 line
Changed paths:
   M /trunk/tabix/bgzip.c

The behaviour changed slightly to mimic gzip. Detect if std descriptors are connected to the terminal.
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r549 | petulda | 2010-04-22 09:46:10 -0400 (Thu, 22 Apr 2010) | 1 line
Changed paths:
   M /trunk/tabix/bgzip.c

Fix in src/dst file detection and slight change of behaviour
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r548 | petulda | 2010-04-19 04:39:46 -0400 (Mon, 19 Apr 2010) | 1 line
Changed paths:
   M /trunk/tabix/index.c

Close file descriptor in ti_list_chromosomes
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r547 | petulda | 2010-04-16 09:27:11 -0400 (Fri, 16 Apr 2010) | 1 line
Changed paths:
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c
   M /trunk/tabix/tabix.h

Added the -l option for listing chromosomes
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r544 | lh3lh3 | 2010-03-29 10:58:48 -0400 (Mon, 29 Mar 2010) | 2 lines
Changed paths:
   M /trunk/tabix/main.c

removed a line of debugging code

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r543 | lh3lh3 | 2010-03-19 12:29:16 -0400 (Fri, 19 Mar 2010) | 3 lines
Changed paths:
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c
   M /trunk/tabix/tabix.1

 * tabix-0.1.3 (r543)
 * fixed another off-by-one bug

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r542 | lh3lh3 | 2010-03-16 22:35:52 -0400 (Tue, 16 Mar 2010) | 2 lines
Changed paths:
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c
   M /trunk/tabix/tabix.1

Release tabix-0.1.1

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r506 | lh3lh3 | 2009-11-02 23:20:12 -0500 (Mon, 02 Nov 2009) | 2 lines
Changed paths:
   M /trunk/tabix/main.c

Release tabix-0.1.0

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r505 | lh3lh3 | 2009-11-02 23:15:49 -0500 (Mon, 02 Nov 2009) | 2 lines
Changed paths:
   A /trunk/tabix/tabix.1

documentation

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r504 | lh3lh3 | 2009-11-02 11:08:18 -0500 (Mon, 02 Nov 2009) | 5 lines
Changed paths:
   M /trunk/tabix/Makefile
   M /trunk/tabix/bgzip.c
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c
   M /trunk/tabix/tabix.h

 * tabix-0.0.0-5 (r504)
 * fixed a critical bug in fetching data (a typo in fact)
 * support SAM (tested on ex1.sam) and VCF (not tested)
 * improve the command-line interface

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r503 | lh3lh3 | 2009-11-02 10:04:43 -0500 (Mon, 02 Nov 2009) | 3 lines
Changed paths:
   M /trunk/tabix/Makefile
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c

 * tabix-0.0.0-4 (r503)
 * index files are bgzf compressed

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r502 | lh3lh3 | 2009-11-02 09:47:25 -0500 (Mon, 02 Nov 2009) | 4 lines
Changed paths:
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c
   M /trunk/tabix/tabix.h

 * tabix-0.0.0-3 (r502)
 * support meta lines (not tested)
 * I am going to make the index file in the BGZF format

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r501 | lh3lh3 | 2009-11-01 22:03:07 -0500 (Sun, 01 Nov 2009) | 3 lines
Changed paths:
   M /trunk/tabix/Makefile
   M /trunk/tabix/bgzf.h
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c

 * tabix-0.0.0-2 (r501)
 * accelerate ti_readline()

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r500 | lh3lh3 | 2009-11-01 20:49:52 -0500 (Sun, 01 Nov 2009) | 3 lines
Changed paths:
   M /trunk/tabix/Makefile
   M /trunk/tabix/bgzip.c
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c

 * tabix-0.0.0-1 (r500)
 * apparently working

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r499 | lh3lh3 | 2009-11-01 14:04:52 -0500 (Sun, 01 Nov 2009) | 2 lines
Changed paths:
   D /trunk/tabix/parser.c

obsolete file

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r498 | lh3lh3 | 2009-11-01 14:04:08 -0500 (Sun, 01 Nov 2009) | 2 lines
Changed paths:
   M /trunk/tabix/bgzip.c

bgzip is more like gzip in its command-line interface

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r497 | lh3lh3 | 2009-11-01 13:43:35 -0500 (Sun, 01 Nov 2009) | 2 lines
Changed paths:
   A /trunk/tabix/Makefile
   A /trunk/tabix/bam_endian.h
   A /trunk/tabix/bgzf.c
   A /trunk/tabix/bgzf.h
   A /trunk/tabix/bgzip.c
   A /trunk/tabix/index.c
   A /trunk/tabix/khash.h
   A /trunk/tabix/knetfile.c
   A /trunk/tabix/knetfile.h
   A /trunk/tabix/ksort.h
   A /trunk/tabix/kstring.c
   A /trunk/tabix/kstring.h
   A /trunk/tabix/main.c
   A /trunk/tabix/parser.c
   A /trunk/tabix/tabix.h

initial source code. It is BUGGY!

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r496 | lh3lh3 | 2009-11-01 13:42:39 -0500 (Sun, 01 Nov 2009) | 2 lines
Changed paths:
   A /trunk/tabix

A generic indexer for TAB-delimited genome position files

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