Revision
263 -
Directory Listing
Modified
Mon Jul 30 21:38:58 2012 UTC
(12 years, 1 month ago)
by
gpertea
resuming works
Revision
262 -
Directory Listing
Modified
Wed Jul 25 20:29:58 2012 UTC
(12 years, 1 month ago)
by
gpertea
wip - tophat adding resume features (need to add setRunStage())
Revision
261 -
Directory Listing
Modified
Tue Jul 24 20:13:46 2012 UTC
(12 years, 1 month ago)
by
gpertea
Revision
260 -
Directory Listing
Modified
Tue Jul 24 20:10:50 2012 UTC
(12 years, 1 month ago)
by
gpertea
wip tophat.py - adding resume feature
Revision
259 -
Directory Listing
Modified
Fri Jun 29 19:01:59 2012 UTC
(12 years, 2 months ago)
by
gpertea
updated to v2.0.4
Revision
257 -
Directory Listing
Modified
Mon Jun 18 21:08:57 2012 UTC
(12 years, 2 months ago)
by
gpertea
update
Revision
256 -
Directory Listing
Modified
Mon Jun 11 19:35:44 2012 UTC
(12 years, 2 months ago)
by
gpertea
sync with Daehwan's fixes
Revision
254 -
Directory Listing
Modified
Wed May 30 22:29:09 2012 UTC
(12 years, 3 months ago)
by
gpertea
fix_map_ordering wip to throw away not "acceptable" mappings
Revision
247 -
Directory Listing
Modified
Thu May 17 03:37:32 2012 UTC
(12 years, 3 months ago)
by
gpertea
fixed the prefilter bug, I think
Revision
246 -
Directory Listing
Modified
Wed May 16 22:42:35 2012 UTC
(12 years, 3 months ago)
by
gpertea
wip, -M option still broken!
Revision
245 -
Directory Listing
Modified
Wed May 16 21:51:01 2012 UTC
(12 years, 3 months ago)
by
gpertea
merge-sync attempt
Revision
244 -
Directory Listing
Modified
Wed May 16 20:38:28 2012 UTC
(12 years, 3 months ago)
by
gpertea
seems to work, before sync
Revision
243 -
Directory Listing
Modified
Wed May 16 16:41:58 2012 UTC
(12 years, 3 months ago)
by
gpertea
wip prep_reads
Revision
242 -
Directory Listing
Modified
Tue May 15 21:37:24 2012 UTC
(12 years, 3 months ago)
by
gpertea
wip!!!
Revision
241 -
Directory Listing
Modified
Tue May 15 01:44:51 2012 UTC
(12 years, 3 months ago)
by
gpertea
wip tophat
Revision
240 -
Directory Listing
Modified
Mon May 14 21:35:52 2012 UTC
(12 years, 3 months ago)
by
gpertea
wip tophat accepted_hits
Revision
239 -
Directory Listing
Modified
Mon May 14 21:01:08 2012 UTC
(12 years, 3 months ago)
by
gpertea
wip prep_reads.cpp, tophat
Revision
238 -
Directory Listing
Modified
Wed May 9 12:14:58 2012 UTC
(12 years, 3 months ago)
by
gpertea
wip
Revision
237 -
Directory Listing
Modified
Mon May 7 23:30:42 2012 UTC
(12 years, 3 months ago)
by
gpertea
wip
Revision
236 -
Directory Listing
Modified
Fri May 4 22:20:02 2012 UTC
(12 years, 4 months ago)
by
gpertea
sync, wip prep_reads
Revision
233 -
Directory Listing
Modified
Wed Apr 11 21:05:01 2012 UTC
(12 years, 4 months ago)
by
gpertea
Revision
231 -
Directory Listing
Modified
Tue Apr 3 21:41:40 2012 UTC
(12 years, 5 months ago)
by
gpertea
resync
Revision
230 -
Directory Listing
Modified
Thu Mar 29 21:44:57 2012 UTC
(12 years, 5 months ago)
by
gpertea
prefilter works, but it eliminates too many reads (!)
Revision
229 -
Directory Listing
Modified
Wed Mar 28 05:19:02 2012 UTC
(12 years, 5 months ago)
by
gpertea
prefiltering seems to work
Revision
228 -
Directory Listing
Modified
Wed Mar 28 05:13:28 2012 UTC
(12 years, 5 months ago)
by
gpertea
wip - prefiltering fix
Revision
223 -
Directory Listing
Modified
Fri Mar 23 22:39:52 2012 UTC
(12 years, 5 months ago)
by
gpertea
Revision
222 -
Directory Listing
Modified
Fri Mar 23 22:39:15 2012 UTC
(12 years, 5 months ago)
by
gpertea
Revision
221 -
Directory Listing
Modified
Fri Mar 23 03:15:08 2012 UTC
(12 years, 5 months ago)
by
gpertea
Revision
220 -
Directory Listing
Modified
Thu Mar 22 19:33:00 2012 UTC
(12 years, 5 months ago)
by
gpertea
working, writing rejected.bam
Revision
219 -
Directory Listing
Modified
Wed Mar 21 21:06:37 2012 UTC
(12 years, 5 months ago)
by
gpertea
almost working with bam all over
Revision
218 -
Directory Listing
Modified
Tue Mar 20 21:31:57 2012 UTC
(12 years, 5 months ago)
by
gpertea
prep_reads now writes bam
Revision
217 -
Directory Listing
Modified
Wed Mar 14 19:58:18 2012 UTC
(12 years, 5 months ago)
by
gpertea
Revision
216 -
Directory Listing
Modified
Wed Mar 14 02:43:25 2012 UTC
(12 years, 5 months ago)
by
gpertea
Revision
215 -
Directory Listing
Modified
Wed Mar 14 02:06:47 2012 UTC
(12 years, 5 months ago)
by
gpertea
bam read support complete, now to make prep_reads conversion..
Revision
212 -
Directory Listing
Modified
Tue Mar 13 21:32:44 2012 UTC
(12 years, 5 months ago)
by
gpertea
misaligned extra bowtie command fixed
Revision
211 -
Directory Listing
Modified
Tue Mar 13 21:02:03 2012 UTC
(12 years, 5 months ago)
by
gpertea
wip -- still errors in logs!
Revision
210 -
Directory Listing
Modified
Tue Mar 13 01:26:20 2012 UTC
(12 years, 5 months ago)
by
gpertea
wip: prep_reads from/to BAM
Revision
209 -
Directory Listing
Modified
Mon Mar 12 23:24:11 2012 UTC
(12 years, 5 months ago)
by
gpertea
Revision
208 -
Directory Listing
Modified
Mon Mar 12 23:11:55 2012 UTC
(12 years, 5 months ago)
by
gpertea
removed symlink
Revision
207 -
Directory Listing
Modified
Mon Mar 12 21:39:30 2012 UTC
(12 years, 5 months ago)
by
gpertea
wip
Revision
206 -
Directory Listing
Modified
Mon Mar 12 18:02:35 2012 UTC
(12 years, 5 months ago)
by
gpertea
updated
Revision
205 -
Directory Listing
Modified
Mon Mar 12 17:40:44 2012 UTC
(12 years, 5 months ago)
by
gpertea
silly bug fix
Revision
204 -
Directory Listing
Modified
Mon Mar 12 15:51:21 2012 UTC
(12 years, 5 months ago)
by
gpertea
more fixes for bam2fastx.cpp
Revision
203 -
Directory Listing
Modified
Mon Mar 12 12:03:12 2012 UTC
(12 years, 5 months ago)
by
gpertea
fixed bam2fastx bugs
Revision
202 -
Directory Listing
Modified
Mon Mar 12 03:59:38 2012 UTC
(12 years, 5 months ago)
by
gpertea
added -P option to write paired reads, and compression
Revision
201 -
Directory Listing
Modified
Sun Mar 11 21:29:20 2012 UTC
(12 years, 5 months ago)
by
gpertea
Revision
200 -
Directory Listing
Modified
Fri Mar 9 22:25:25 2012 UTC
(12 years, 5 months ago)
by
gpertea
Revision
169 -
Directory Listing
Modified
Fri Feb 10 18:56:56 2012 UTC
(12 years, 6 months ago)
by
gpertea
sync
Revision
168 -
Directory Listing
Modified
Fri Feb 10 16:40:38 2012 UTC
(12 years, 6 months ago)
by
gpertea
finally fixed bam_merge
Revision
167 -
Directory Listing
Modified
Fri Feb 10 05:51:56 2012 UTC
(12 years, 6 months ago)
by
gpertea
bam_merge needs fixing!
Revision
166 -
Directory Listing
Modified
Fri Feb 10 02:45:06 2012 UTC
(12 years, 6 months ago)
by
gpertea
resync
Revision
165 -
Directory Listing
Modified
Fri Feb 10 01:04:05 2012 UTC
(12 years, 6 months ago)
by
gpertea
sync back with Daehwan. Test bam_merge for memory leaks!
Revision
164 -
Directory Listing
Modified
Thu Feb 9 05:30:41 2012 UTC
(12 years, 6 months ago)
by
gpertea
wip
Revision
163 -
Directory Listing
Modified
Thu Feb 9 03:31:49 2012 UTC
(12 years, 6 months ago)
by
gpertea
wip
Revision
159 -
Directory Listing
Modified
Mon Jan 30 22:38:08 2012 UTC
(12 years, 7 months ago)
by
gpertea
wip
Revision
158 -
Directory Listing
Modified
Sun Jan 29 19:42:10 2012 UTC
(12 years, 7 months ago)
by
gpertea
Revision
157 -
Directory Listing
Modified
Fri Jan 27 22:33:06 2012 UTC
(12 years, 7 months ago)
by
gpertea
added index writing to GBamWriter
Revision
154 -
Directory Listing
Modified
Tue Jan 24 02:29:21 2012 UTC
(12 years, 7 months ago)
by
gpertea
massive update with Daehwan's work
Revision
140 -
Directory Listing
Modified
Thu Dec 15 22:40:48 2011 UTC
(12 years, 8 months ago)
by
gpertea
Revision
139 -
Directory Listing
Modified
Thu Dec 15 22:36:13 2011 UTC
(12 years, 8 months ago)
by
gpertea
spliceCigar() implemented, needs testing
Revision
138 -
Directory Listing
Modified
Wed Dec 14 22:58:39 2011 UTC
(12 years, 8 months ago)
by
gpertea
Revision
137 -
Directory Listing
Modified
Wed Dec 14 22:58:22 2011 UTC
(12 years, 8 months ago)
by
gpertea
wip spliceCigar() in bwt_map.cpp needs testing
Revision
135 -
Directory Listing
Modified
Mon Dec 12 22:28:38 2011 UTC
(12 years, 8 months ago)
by
gpertea
wip - SplicedSAMHitFactory() still not implemented
Revision
111 -
Directory Listing
Modified
Tue Oct 25 17:05:09 2011 UTC
(12 years, 10 months ago)
by
gpertea
wip
Revision
97 -
Directory Listing
Modified
Thu Oct 6 19:45:36 2011 UTC
(12 years, 10 months ago)
by
gpertea
by default bam2fastx shows unmapped only
Revision
70 -
Directory Listing
Modified
Tue Sep 20 19:32:58 2011 UTC
(12 years, 11 months ago)
by
gpertea
wip : spliceCigar()
Revision
69 -
Directory Listing
Modified
Mon Sep 19 21:00:41 2011 UTC
(12 years, 11 months ago)
by
gpertea
wip - implementing SplicedSAMHitFactory::get_hit_from_buf()
Revision
68 -
Directory Listing
Modified
Mon Sep 19 20:09:26 2011 UTC
(12 years, 11 months 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
(12 years, 11 months ago)
by
gpertea
fixed segment_juncs to work with .bam files
Revision
37 -
Directory Listing
Modified
Mon Aug 22 16:17:34 2011 UTC
(13 years ago)
by
gpertea
wip
Revision
35 -
Directory Listing
Modified
Fri Aug 5 18:47:20 2011 UTC
(13 years, 1 month ago)
by
gpertea
wip
Revision
34 -
Directory Listing
Modified
Wed Aug 3 22:15:52 2011 UTC
(13 years, 1 month ago)
by
gpertea
wip segment_juncs
Revision
33 -
Directory Listing
Modified
Wed Aug 3 17:02:56 2011 UTC
(13 years, 1 month ago)
by
gpertea
wip conversion to SAM processing
Revision
32 -
Directory Listing
Modified
Tue Aug 2 22:04:47 2011 UTC
(13 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
(13 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
(13 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
(13 years, 1 month ago)
by
gpertea
adding tophat source work
Revision
28 -
Directory Listing
Added
Tue Aug 2 21:23:26 2011 UTC
(13 years, 1 month ago)
by
gpertea
adding tophat_cpp dir