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ChangeLog
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ChangeLog
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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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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.*
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
r580 | lh3lh3 | 2010-05-23 23:36:05 -0400 (Sun, 23 May 2010) | 2 lines
Changed paths:
M /trunk/tabix/tabix.py
minor change
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
r573 | lh3lh3 | 2010-05-11 12:08:30 -0400 (Tue, 11 May 2010) | 2 lines
Changed paths:
M /trunk/tabix/Makefile
Added -fPIC
------------------------------------------------------------------------
r572 | lh3lh3 | 2010-05-11 11:59:07 -0400 (Tue, 11 May 2010) | 2 lines
Changed paths:
M /trunk/tabix/perl/MANIFEST
update
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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()
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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)
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
r505 | lh3lh3 | 2009-11-02 23:15:49 -0500 (Mon, 02 Nov 2009) | 2 lines
Changed paths:
A /trunk/tabix/tabix.1
documentation
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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()
------------------------------------------------------------------------
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
------------------------------------------------------------------------
r499 | lh3lh3 | 2009-11-01 14:04:52 -0500 (Sun, 01 Nov 2009) | 2 lines
Changed paths:
D /trunk/tabix/parser.c
obsolete file
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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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