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Revision 83 - Directory Listing
Modified Thu Sep 29 21:32:42 2011 UTC (9 years, 11 months ago) by gpertea
wip

Revision 82 - Directory Listing
Modified Thu Sep 29 20:46:39 2011 UTC (9 years, 11 months ago) by gpertea
wip

Revision 81 - Directory Listing
Modified Thu Sep 29 19:02:24 2011 UTC (9 years, 11 months ago) by gpertea
fixes, still a bug with flast_d[d] = flast_d[d] - flower + 2;

Revision 80 - Directory Listing
Modified Wed Sep 28 21:12:17 2011 UTC (9 years, 11 months ago) by gpertea
wip

Revision 79 - Directory Listing
Modified Wed Sep 28 19:54:42 2011 UTC (9 years, 11 months ago) by gpertea
wip, fixed memory leaks

Revision 78 - Directory Listing
Modified Wed Sep 28 03:20:10 2011 UTC (9 years, 11 months ago) by gpertea
3' match seems to work, needs a few refinements

Revision 77 - Directory Listing
Modified Tue Sep 27 21:07:59 2011 UTC (9 years, 11 months ago) by gpertea
wip - cutting seeds, finalize()

Revision 76 - Directory Listing
Modified Tue Sep 27 12:37:02 2011 UTC (9 years, 11 months ago) by gpertea
u

Revision 75 - Directory Listing
Modified Tue Sep 27 02:24:57 2011 UTC (9 years, 11 months ago) by gpertea
implementing GreedyAlign for best rseeds etc.

Revision 74 - Directory Listing
Modified Tue Sep 27 01:22:37 2011 UTC (9 years, 11 months ago) by gpertea
added seqalign files

Revision 73 - Directory Listing
Modified Tue Sep 27 01:20:53 2011 UTC (9 years, 11 months ago) by gpertea
creating seqalign storage

Revision 72 - Directory Listing
Modified Tue Sep 27 01:20:21 2011 UTC (9 years, 11 months ago) by gpertea
reversed gene_id requirement for TSS clustering

Revision 71 - Directory Listing
Modified Fri Sep 23 19:23:49 2011 UTC (10 years ago) by gpertea
gridx fixed to export PERL5LIB and PYTHONPATH

Revision 70 - Directory Listing
Modified Tue Sep 20 19:32:58 2011 UTC (10 years ago) by gpertea
wip : spliceCigar()

Revision 69 - Directory Listing
Modified Mon Sep 19 21:00:41 2011 UTC (10 years ago) by gpertea
wip - implementing SplicedSAMHitFactory::get_hit_from_buf()

Revision 68 - Directory Listing
Modified Mon Sep 19 20:09:26 2011 UTC (10 years ago) by gpertea
first attempt at accepting different Color qvlen in prep_reads

Revision 67 - Directory Listing
Modified Mon Sep 19 19:39:49 2011 UTC (10 years ago) by gpertea
fixed segment_juncs to work with .bam files

Revision 66 - Directory Listing
Modified Fri Sep 16 18:33:54 2011 UTC (10 years ago) by gpertea
made some Flybase GFF3 "errors" non-fatal

Revision 65 - Directory Listing
Modified Fri Sep 16 18:33:19 2011 UTC (10 years ago) by gpertea

Revision 64 - Directory Listing
Modified Fri Sep 9 20:58:16 2011 UTC (10 years ago) by gpertea
made sure the order of XLoci is maintained during clustering

Revision 63 - Directory Listing
Modified Fri Sep 9 20:19:21 2011 UTC (10 years ago) by gpertea

Revision 62 - Directory Listing
Modified Fri Sep 9 20:19:10 2011 UTC (10 years ago) by gpertea
added --force-exons option to force "exon" subfeatures

Revision 61 - Directory Listing
Modified Fri Sep 9 18:46:01 2011 UTC (10 years ago) by gpertea
removed startChanged flag, not needed

Revision 60 - Directory Listing
Modified Fri Sep 9 18:00:55 2011 UTC (10 years ago) by gpertea
made sure Swap (Exchange) is available for GList, GVec

Revision 59 - Directory Listing
Modified Fri Sep 9 18:00:23 2011 UTC (10 years ago) by gpertea
finally fixed the placeGf clustering bug

Revision 58 - Directory Listing
Modified Fri Sep 9 14:01:30 2011 UTC (10 years ago) by gpertea
fixed buglet in fix_umrnas() comparing strand to 0 instead of '.'

Revision 57 - Directory Listing
Modified Thu Sep 8 11:52:37 2011 UTC (10 years ago) by gpertea
wip

Revision 56 - Directory Listing
Modified Thu Sep 8 05:47:09 2011 UTC (10 years ago) by gpertea
RPS20P29, ENSG00000241828 not collapsing

Revision 55 - Directory Listing
Modified Thu Sep 8 05:46:53 2011 UTC (10 years ago) by gpertea
RPS20P29, ENSG00000241828 not collapsing

Revision 54 - Directory Listing
Modified Thu Sep 8 05:46:16 2011 UTC (10 years ago) by gpertea
debug RPS20P29 ENSG00000241828 not collapsing

Revision 53 - Directory Listing
Modified Thu Sep 8 02:43:56 2011 UTC (10 years ago) by gpertea

Revision 52 - Directory Listing
Modified Thu Sep 8 02:43:30 2011 UTC (10 years ago) by gpertea
reclass_XStrand fixed for 's' not code being reported if 'i' was found

Revision 51 - Directory Listing
Modified Thu Sep 8 01:02:11 2011 UTC (10 years ago) by gpertea
fix direct CDS segment given as the only subfeature

Revision 50 - Directory Listing
Modified Thu Sep 8 00:47:22 2011 UTC (10 years ago) by gpertea
fixed a loading bug when a CDS was given to a monoFeature() with a self-exon

Revision 49 - Directory Listing
Modified Wed Sep 7 16:26:02 2011 UTC (10 years ago) by gpertea
minor edits

Revision 48 - Directory Listing
Modified Wed Sep 7 16:07:32 2011 UTC (10 years ago) by gpertea
longest CDS is now kept on -MK containment

Revision 47 - Directory Listing
Modified Wed Sep 7 01:12:20 2011 UTC (10 years ago) by gpertea
when collapsing redundant transcripts, transfer CDS coords to the container if it doesn't have any

Revision 46 - Directory Listing
Modified Wed Sep 7 00:00:08 2011 UTC (10 years ago) by gpertea
fixed GStr[-2] bug

Revision 45 - Directory Listing
Modified Tue Sep 6 18:19:20 2011 UTC (10 years ago) by gpertea
added gfview files

Revision 44 - Directory Listing
Modified Tue Sep 6 18:15:55 2011 UTC (10 years ago) by gpertea
added gfview

Revision 43 - Directory Listing
Modified Tue Sep 6 17:41:50 2011 UTC (10 years ago) by gpertea
m

Revision 42 - Directory Listing
Modified Tue Sep 6 17:40:45 2011 UTC (10 years ago) by gpertea
minor edit

Revision 41 - Directory Listing
Modified Sat Aug 27 16:58:00 2011 UTC (10 years ago) by gpertea
added fix for fileExists() under MSVC

Revision 40 - Directory Listing
Modified Sat Aug 27 16:48:50 2011 UTC (10 years ago) by gpertea
added clview files and examples

Revision 39 - Directory Listing
Modified Sat Aug 27 15:50:52 2011 UTC (10 years ago) by gpertea
clview added

Revision 38 - Directory Listing
Modified Sat Aug 27 15:42:15 2011 UTC (10 years ago) by gpertea

Revision 37 - Directory Listing
Modified Mon Aug 22 16:17:34 2011 UTC (10 years, 1 month ago) by gpertea
wip

Revision 36 - Directory Listing
Modified Mon Aug 22 15:56:21 2011 UTC (10 years, 1 month ago) by gpertea

Revision 35 - Directory Listing
Modified Fri Aug 5 18:47:20 2011 UTC (10 years, 1 month ago) by gpertea
wip

Revision 34 - Directory Listing
Modified Wed Aug 3 22:15:52 2011 UTC (10 years, 1 month ago) by gpertea
wip segment_juncs

Revision 33 - Directory Listing
Modified Wed Aug 3 17:02:56 2011 UTC (10 years, 1 month ago) by gpertea
wip conversion to SAM processing

Revision 32 - Directory Listing
Modified Tue Aug 2 22:04:47 2011 UTC (10 years, 1 month ago) by gpertea
adding bam2fastx as recognized unpacker for .bam files

Revision 31 - Directory Listing
Modified Tue Aug 2 21:58:18 2011 UTC (10 years, 1 month ago) by gpertea
trying to get rid of unspliced_bwt in Maps (replace by unspliced_sam)

Revision 30 - Directory Listing
Modified Tue Aug 2 21:25:50 2011 UTC (10 years, 1 month ago) by gpertea
added SeqAn to tophat source pack

Revision 29 - Directory Listing
Modified Tue Aug 2 21:24:54 2011 UTC (10 years, 1 month ago) by gpertea
adding tophat source work

Revision 28 - Directory Listing
Modified Tue Aug 2 21:23:26 2011 UTC (10 years, 1 month ago) by gpertea
adding tophat_cpp dir

Revision 27 - Directory Listing
Modified Wed Jul 27 20:43:37 2011 UTC (10 years, 1 month ago) by gpertea

Revision 26 - Directory Listing
Modified Wed Jul 27 19:39:27 2011 UTC (10 years, 1 month ago) by gpertea
added missing gff_utils source

Revision 25 - Directory Listing
Modified Tue Jul 26 21:50:53 2011 UTC (10 years, 1 month ago) by gpertea

Revision 24 - Directory Listing
Modified Tue Jul 26 21:46:39 2011 UTC (10 years, 1 month ago) by gpertea

Revision 23 - Directory Listing
Modified Tue Jul 26 21:44:38 2011 UTC (10 years, 1 month ago) by gpertea
adding misc scripts

Revision 22 - Directory Listing
Modified Tue Jul 26 21:43:45 2011 UTC (10 years, 1 month ago) by gpertea
various scripts

Revision 21 - Directory Listing
Modified Mon Jul 18 22:35:05 2011 UTC (10 years, 2 months ago) by gpertea
added recent fix for no TSS-cluster if different GeneID

Revision 20 - Directory Listing
Modified Mon Jul 18 21:08:36 2011 UTC (10 years, 2 months ago) by gpertea
added cuffcompare sources

Revision 19 - Directory Listing
Modified Mon Jul 18 21:07:43 2011 UTC (10 years, 2 months ago) by gpertea
mkdir cuffcompare

Revision 18 - Directory Listing
Modified Mon Jul 18 21:00:21 2011 UTC (10 years, 2 months ago) by gpertea
added a few more source files, test code

Revision 17 - Directory Listing
Modified Mon Jul 18 20:57:05 2011 UTC (10 years, 2 months ago) by gpertea
sync with local source

Revision 16 - Directory Listing
Modified Mon Jul 18 20:56:02 2011 UTC (10 years, 2 months ago) by gpertea
sync with local source

Revision 15 - Directory Listing
Modified Mon Jul 18 20:53:45 2011 UTC (10 years, 2 months ago) by gpertea
sync with local src

Revision 14 - Directory Listing
Modified Mon Jul 18 20:36:48 2011 UTC (10 years, 2 months ago) by gpertea
added old trimpoly code just for archive

Revision 13 - Directory Listing
Modified Mon Jul 18 20:35:43 2011 UTC (10 years, 2 months ago) by gpertea
sync with my local source

Revision 12 - Directory Listing
Modified Wed Jan 26 19:05:05 2011 UTC (10 years, 7 months ago) by gpertea
added qv-threshold trimming

Revision 11 - Directory Listing
Modified Tue Mar 23 18:03:12 2010 UTC (11 years, 6 months ago) by gpertea
update l5,l3 to defaults if no trimming is performed

Revision 10 - Directory Listing
Modified Tue Mar 23 17:46:56 2010 UTC (11 years, 6 months ago) by gpertea
bugfix: prevent crash with -o option is not given

Revision 9 - Directory Listing
Modified Tue Mar 23 17:12:14 2010 UTC (11 years, 6 months ago) by gpertea
fixed bug causing overtrimming

Revision 8 - Directory Listing
Modified Mon Mar 22 22:11:25 2010 UTC (11 years, 6 months ago) by gpertea
added cdbfasta source files

Revision 7 - Directory Listing
Modified Mon Mar 22 22:08:51 2010 UTC (11 years, 6 months ago) by gpertea
mkdir cdbfasta

Revision 6 - Directory Listing
Modified Mon Mar 22 22:07:27 2010 UTC (11 years, 6 months ago) by gpertea
added gffread sources

Revision 5 - Directory Listing
Modified Mon Mar 22 22:06:27 2010 UTC (11 years, 6 months ago) by gpertea
mkdir gffread

Revision 4 - Directory Listing
Modified Mon Mar 22 22:05:23 2010 UTC (11 years, 6 months ago) by gpertea
initial commit

Revision 3 - Directory Listing
Modified Mon Mar 22 22:04:34 2010 UTC (11 years, 6 months ago) by gpertea
mkdir

Revision 2 - Directory Listing
Modified Mon Mar 22 22:03:27 2010 UTC (11 years, 6 months ago) by gpertea
added my gclib source files

Revision 1 - Directory Listing
Added Mon Mar 22 22:01:50 2010 UTC (11 years, 6 months ago) by gpertea
import