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r942 | lh3lh3 | 2011-03-31 16:39:50 -0400 (Thu, 31 Mar 2011) | 2 lines
Changed paths:
   M /trunk/tabix/main.c

update version number

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r940 | lh3lh3 | 2011-03-31 16:38:03 -0400 (Thu, 31 Mar 2011) | 2 lines
Changed paths:
   M /trunk/tabix/bedidx.c
   M /trunk/tabix/main.c

fixed two bugs due to recent changes

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r939 | lh3lh3 | 2011-03-31 16:12:21 -0400 (Thu, 31 Mar 2011) | 2 lines
Changed paths:
   M /trunk/tabix/bgzf.c
   M /trunk/tabix/bgzf.h
   M /trunk/tabix/main.c

update to the latest bgzf.*

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r938 | lh3lh3 | 2011-03-31 16:02:21 -0400 (Thu, 31 Mar 2011) | 2 lines
Changed paths:
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c
   M /trunk/tabix/tabix.h

BED support

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r937 | lh3lh3 | 2011-03-31 15:03:49 -0400 (Thu, 31 Mar 2011) | 2 lines
Changed paths:
   M /trunk/tabix/Makefile
   A /trunk/tabix/bedidx.c
   M /trunk/tabix/example.gtf.gz.tbi
   M /trunk/tabix/index.c
   A /trunk/tabix/kseq.h
   M /trunk/tabix/tabix.h

restructure get_intv() for BED support

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r919 | petulda | 2011-02-24 10:14:14 -0500 (Thu, 24 Feb 2011) | 1 line
Changed paths:
   M /trunk/tabix/bgzf.c
   M /trunk/tabix/bgzf.h
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c

New -r (reheader) option for efficient header replacement.
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r915 | lh3lh3 | 2011-02-22 09:50:57 -0500 (Tue, 22 Feb 2011) | 2 lines
Changed paths:
   A /trunk/tabix/python
   A /trunk/tabix/python/setup.py (from /trunk/tabix/setup.py:914)
   A /trunk/tabix/python/tabixmodule.c (from /trunk/tabix/tabixmodule.c:914)
   A /trunk/tabix/python/test.py (from /trunk/tabix/test.py:914)
   D /trunk/tabix/setup.py
   D /trunk/tabix/tabixmodule.c
   D /trunk/tabix/test.py

move to a new python/ directory

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r914 | lh3lh3 | 2011-02-22 09:49:35 -0500 (Tue, 22 Feb 2011) | 2 lines
Changed paths:
   A /trunk/tabix/setup.py
   A /trunk/tabix/tabixmodule.c
   A /trunk/tabix/test.py

CPython C-API by Hyeshik Chang

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r904 | petulda | 2011-01-28 08:06:27 -0500 (Fri, 28 Jan 2011) | 1 line
Changed paths:
   M /trunk/tabix/index.c

Check the number of fields on each line and exit nicely without segfault
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r901 | petulda | 2011-01-21 06:45:37 -0500 (Fri, 21 Jan 2011) | 1 line
Changed paths:
   M /trunk/tabix/main.c

Fix: Complain only when VCF is newer, not newer or same mtime
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r900 | petulda | 2011-01-21 04:23:04 -0500 (Fri, 21 Jan 2011) | 1 line
Changed paths:
   M /trunk/tabix/main.c

Prevent the common user mistake and check the timestamps of the vcf and index file
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r876 | lh3lh3 | 2010-12-08 12:38:45 -0500 (Wed, 08 Dec 2010) | 2 lines
Changed paths:
   M /trunk/tabix/ChangeLog
   M /trunk/tabix/NEWS
   M /trunk/tabix/main.c

Release tabix-0.2.3

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r875 | lh3lh3 | 2010-12-08 12:28:35 -0500 (Wed, 08 Dec 2010) | 2 lines
Changed paths:
   M /trunk/tabix/ChangeLog
   M /trunk/tabix/index.c

Fixed a minor bug in generating index

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r855 | petulda | 2010-11-25 11:50:13 -0500 (Thu, 25 Nov 2010) | 1 line
Changed paths:
   M /trunk/tabix/main.c

Disable "unknown target name or minus interval" warning.
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r775 | petulda | 2010-10-26 15:02:30 -0400 (Tue, 26 Oct 2010) | 1 line
Changed paths:
   M /trunk/tabix/main.c

Added -h option to print header lines
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r742 | jmarshall | 2010-09-27 06:47:23 -0400 (Mon, 27 Sep 2010) | 2 lines
Changed paths:
   M /trunk/tabix

Add svn:ignore properties for intermediate and generated files.

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r725 | lh3lh3 | 2010-09-15 13:01:53 -0400 (Wed, 15 Sep 2010) | 2 lines
Changed paths:
   M /trunk/tabix/bgzip.c

patches by Peter Chines

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r714 | lh3lh3 | 2010-09-07 10:13:25 -0400 (Tue, 07 Sep 2010) | 2 lines
Changed paths:
   M /trunk/tabix/TabixReader.java
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c

fixed a bug in C/Java when n_off == 0

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r712 | lh3lh3 | 2010-09-03 09:21:23 -0400 (Fri, 03 Sep 2010) | 2 lines
Changed paths:
   M /trunk/tabix/TabixReader.java

fixed a bug in parsing region strings

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r700 | petulda | 2010-08-25 10:42:37 -0400 (Wed, 25 Aug 2010) | 1 line
Changed paths:
   M /trunk/tabix/main.c

Fix: Exit with an error rather than segfault when index is not present and region is queried
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r696 | petulda | 2010-08-24 10:24:12 -0400 (Tue, 24 Aug 2010) | 1 line
Changed paths:
   M /trunk/tabix/bgzf.c
   M /trunk/tabix/bgzf.h
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c

Complain about not-bgzipped files and check for noncontinuous chromosome blocks
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r603 | lh3lh3 | 2010-06-28 10:49:39 -0400 (Mon, 28 Jun 2010) | 2 lines
Changed paths:
   M /trunk/tabix/NEWS
   M /trunk/tabix/TabixReader.java
   M /trunk/tabix/index.c
   M /trunk/tabix/main.c

Release tabix-0.2.2

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r597 | lh3lh3 | 2010-06-13 21:08:29 -0400 (Sun, 13 Jun 2010) | 3 lines
Changed paths:
   M /trunk/tabix/index.c

Change the namespace of sorting, to avoid function name collision with samtools.


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r582 | lh3lh3 | 2010-06-03 10:40:25 -0400 (Thu, 03 Jun 2010) | 2 lines
Changed paths:
   M /trunk/tabix/NEWS
   M /trunk/tabix/main.c
   M /trunk/tabix/tabix.py

Release tabix-0.2.1

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r581 | lh3lh3 | 2010-05-24 14:24:24 -0400 (Mon, 24 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/tabix.py

OOP interface with the help from Aaron Quinlan

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r580 | lh3lh3 | 2010-05-23 23:36:05 -0400 (Sun, 23 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/tabix.py

minor change

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r579 | lh3lh3 | 2010-05-23 23:25:24 -0400 (Sun, 23 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/tabix.py

For Snow Leopard compatibility

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r575 | lh3lh3 | 2010-05-12 19:31:27 -0400 (Wed, 12 May 2010) | 4 lines
Changed paths:
   M /trunk/tabix/Makefile
   M /trunk/tabix/index.c
   M /trunk/tabix/tabix.h
   A /trunk/tabix/tabix.py

 * optionally generate shared library for Mac and Linux
 * added a python script that directly calls the shared library
 * added a new API for easy python access

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r574 | lh3lh3 | 2010-05-11 12:14:27 -0400 (Tue, 11 May 2010) | 2 lines
Changed paths:
   M /trunk/tabix/ChangeLog
   M /trunk/tabix/NEWS
   M /trunk/tabix/perl/Tabix.pm
   M /trunk/tabix/perl/TabixIterator.pm
   M /trunk/tabix/tabix.1

Release tabix-0.2.0

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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

------------------------------------------------------------------------