X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=ChangeLog;h=3594496ca8de7d1d15535d07a4d329f2504847fe;hb=057cb6e8c54a6e16e47a839ab4ae89ad6f04c731;hp=19d4f3e1d2b78c86248b9d0a0b2ec996a9b63500;hpb=d1fcb739b58e050328dcfc47c3af235bc0e41455;p=tabix.git diff --git a/ChangeLog b/ChangeLog index 19d4f3e..3594496 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,240 @@ +------------------------------------------------------------------------ +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: