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Revision 263 - Directory Listing
Modified Mon Jul 30 21:38:58 2012 UTC (3 years, 9 months ago) by gpertea
resuming works

Revision 262 - Directory Listing
Modified Wed Jul 25 20:29:58 2012 UTC (3 years, 10 months 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 (3 years, 10 months ago) by gpertea

Revision 260 - Directory Listing
Modified Tue Jul 24 20:10:50 2012 UTC (3 years, 10 months ago) by gpertea
wip tophat.py - adding resume feature

Revision 259 - Directory Listing
Modified Fri Jun 29 19:01:59 2012 UTC (3 years, 11 months ago) by gpertea
updated to v2.0.4

Revision 257 - Directory Listing
Modified Mon Jun 18 21:08:57 2012 UTC (3 years, 11 months ago) by gpertea
update

Revision 256 - Directory Listing
Modified Mon Jun 11 19:35:44 2012 UTC (3 years, 11 months ago) by gpertea
sync with Daehwan's fixes

Revision 254 - Directory Listing
Modified Wed May 30 22:29:09 2012 UTC (3 years, 11 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 (4 years ago) by gpertea
fixed the prefilter bug, I think

Revision 246 - Directory Listing
Modified Wed May 16 22:42:35 2012 UTC (4 years ago) by gpertea
wip, -M option still broken!

Revision 245 - Directory Listing
Modified Wed May 16 21:51:01 2012 UTC (4 years ago) by gpertea
merge-sync attempt

Revision 244 - Directory Listing
Modified Wed May 16 20:38:28 2012 UTC (4 years ago) by gpertea
seems to work, before sync

Revision 243 - Directory Listing
Modified Wed May 16 16:41:58 2012 UTC (4 years ago) by gpertea
wip prep_reads

Revision 242 - Directory Listing
Modified Tue May 15 21:37:24 2012 UTC (4 years ago) by gpertea
wip!!!

Revision 241 - Directory Listing
Modified Tue May 15 01:44:51 2012 UTC (4 years ago) by gpertea
wip tophat

Revision 240 - Directory Listing
Modified Mon May 14 21:35:52 2012 UTC (4 years ago) by gpertea
wip tophat accepted_hits

Revision 239 - Directory Listing
Modified Mon May 14 21:01:08 2012 UTC (4 years ago) by gpertea
wip prep_reads.cpp, tophat

Revision 238 - Directory Listing
Modified Wed May 9 12:14:58 2012 UTC (4 years ago) by gpertea
wip

Revision 237 - Directory Listing
Modified Mon May 7 23:30:42 2012 UTC (4 years ago) by gpertea
wip

Revision 236 - Directory Listing
Modified Fri May 4 22:20:02 2012 UTC (4 years ago) by gpertea
sync, wip prep_reads

Revision 233 - Directory Listing
Modified Wed Apr 11 21:05:01 2012 UTC (4 years, 1 month ago) by gpertea

Revision 231 - Directory Listing
Modified Tue Apr 3 21:41:40 2012 UTC (4 years, 1 month ago) by gpertea
resync

Revision 230 - Directory Listing
Modified Thu Mar 29 21:44:57 2012 UTC (4 years, 2 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 (4 years, 2 months ago) by gpertea
prefiltering seems to work

Revision 228 - Directory Listing
Modified Wed Mar 28 05:13:28 2012 UTC (4 years, 2 months ago) by gpertea
wip - prefiltering fix

Revision 223 - Directory Listing
Modified Fri Mar 23 22:39:52 2012 UTC (4 years, 2 months ago) by gpertea

Revision 222 - Directory Listing
Modified Fri Mar 23 22:39:15 2012 UTC (4 years, 2 months ago) by gpertea

Revision 221 - Directory Listing
Modified Fri Mar 23 03:15:08 2012 UTC (4 years, 2 months ago) by gpertea

Revision 220 - Directory Listing
Modified Thu Mar 22 19:33:00 2012 UTC (4 years, 2 months ago) by gpertea
working, writing rejected.bam

Revision 219 - Directory Listing
Modified Wed Mar 21 21:06:37 2012 UTC (4 years, 2 months ago) by gpertea
almost working with bam all over

Revision 218 - Directory Listing
Modified Tue Mar 20 21:31:57 2012 UTC (4 years, 2 months ago) by gpertea
prep_reads now writes bam

Revision 217 - Directory Listing
Modified Wed Mar 14 19:58:18 2012 UTC (4 years, 2 months ago) by gpertea

Revision 216 - Directory Listing
Modified Wed Mar 14 02:43:25 2012 UTC (4 years, 2 months ago) by gpertea

Revision 215 - Directory Listing
Modified Wed Mar 14 02:06:47 2012 UTC (4 years, 2 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 (4 years, 2 months ago) by gpertea
misaligned extra bowtie command fixed

Revision 211 - Directory Listing
Modified Tue Mar 13 21:02:03 2012 UTC (4 years, 2 months ago) by gpertea
wip -- still errors in logs!

Revision 210 - Directory Listing
Modified Tue Mar 13 01:26:20 2012 UTC (4 years, 2 months ago) by gpertea
wip: prep_reads from/to BAM

Revision 209 - Directory Listing
Modified Mon Mar 12 23:24:11 2012 UTC (4 years, 2 months ago) by gpertea

Revision 208 - Directory Listing
Modified Mon Mar 12 23:11:55 2012 UTC (4 years, 2 months ago) by gpertea
removed symlink

Revision 207 - Directory Listing
Modified Mon Mar 12 21:39:30 2012 UTC (4 years, 2 months ago) by gpertea
wip 

Revision 206 - Directory Listing
Modified Mon Mar 12 18:02:35 2012 UTC (4 years, 2 months ago) by gpertea
updated

Revision 205 - Directory Listing
Modified Mon Mar 12 17:40:44 2012 UTC (4 years, 2 months ago) by gpertea
silly bug fix

Revision 204 - Directory Listing
Modified Mon Mar 12 15:51:21 2012 UTC (4 years, 2 months ago) by gpertea
more fixes for bam2fastx.cpp

Revision 203 - Directory Listing
Modified Mon Mar 12 12:03:12 2012 UTC (4 years, 2 months ago) by gpertea
fixed bam2fastx bugs

Revision 202 - Directory Listing
Modified Mon Mar 12 03:59:38 2012 UTC (4 years, 2 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 (4 years, 2 months ago) by gpertea

Revision 200 - Directory Listing
Modified Fri Mar 9 22:25:25 2012 UTC (4 years, 2 months ago) by gpertea

Revision 169 - Directory Listing
Modified Fri Feb 10 18:56:56 2012 UTC (4 years, 3 months ago) by gpertea
sync

Revision 168 - Directory Listing
Modified Fri Feb 10 16:40:38 2012 UTC (4 years, 3 months ago) by gpertea
finally fixed bam_merge

Revision 167 - Directory Listing
Modified Fri Feb 10 05:51:56 2012 UTC (4 years, 3 months ago) by gpertea
bam_merge needs fixing!

Revision 166 - Directory Listing
Modified Fri Feb 10 02:45:06 2012 UTC (4 years, 3 months ago) by gpertea
resync

Revision 165 - Directory Listing
Modified Fri Feb 10 01:04:05 2012 UTC (4 years, 3 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 (4 years, 3 months ago) by gpertea
wip

Revision 163 - Directory Listing
Modified Thu Feb 9 03:31:49 2012 UTC (4 years, 3 months ago) by gpertea
wip

Revision 159 - Directory Listing
Modified Mon Jan 30 22:38:08 2012 UTC (4 years, 3 months ago) by gpertea
wip

Revision 158 - Directory Listing
Modified Sun Jan 29 19:42:10 2012 UTC (4 years, 4 months ago) by gpertea

Revision 157 - Directory Listing
Modified Fri Jan 27 22:33:06 2012 UTC (4 years, 4 months ago) by gpertea
added index writing to GBamWriter

Revision 154 - Directory Listing
Modified Tue Jan 24 02:29:21 2012 UTC (4 years, 4 months ago) by gpertea
massive update with Daehwan's work

Revision 140 - Directory Listing
Modified Thu Dec 15 22:40:48 2011 UTC (4 years, 5 months ago) by gpertea

Revision 139 - Directory Listing
Modified Thu Dec 15 22:36:13 2011 UTC (4 years, 5 months ago) by gpertea
spliceCigar() implemented, needs testing

Revision 138 - Directory Listing
Modified Wed Dec 14 22:58:39 2011 UTC (4 years, 5 months ago) by gpertea

Revision 137 - Directory Listing
Modified Wed Dec 14 22:58:22 2011 UTC (4 years, 5 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 (4 years, 5 months ago) by gpertea
wip - SplicedSAMHitFactory() still not implemented

Revision 111 - Directory Listing
Modified Tue Oct 25 17:05:09 2011 UTC (4 years, 7 months ago) by gpertea
wip

Revision 97 - Directory Listing
Modified Thu Oct 6 19:45:36 2011 UTC (4 years, 7 months ago) by gpertea
by default bam2fastx shows unmapped only

Revision 70 - Directory Listing
Modified Tue Sep 20 19:32:58 2011 UTC (4 years, 8 months ago) by gpertea
wip : spliceCigar()

Revision 69 - Directory Listing
Modified Mon Sep 19 21:00:41 2011 UTC (4 years, 8 months ago) by gpertea
wip - implementing SplicedSAMHitFactory::get_hit_from_buf()

Revision 68 - Directory Listing
Modified Mon Sep 19 20:09:26 2011 UTC (4 years, 8 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 (4 years, 8 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 (4 years, 9 months ago) by gpertea
wip

Revision 35 - Directory Listing
Modified Fri Aug 5 18:47:20 2011 UTC (4 years, 9 months ago) by gpertea
wip

Revision 34 - Directory Listing
Modified Wed Aug 3 22:15:52 2011 UTC (4 years, 9 months ago) by gpertea
wip segment_juncs

Revision 33 - Directory Listing
Modified Wed Aug 3 17:02:56 2011 UTC (4 years, 9 months ago) by gpertea
wip conversion to SAM processing

Revision 32 - Directory Listing
Modified Tue Aug 2 22:04:47 2011 UTC (4 years, 9 months ago) by gpertea
adding bam2fastx as recognized unpacker for .bam files

Revision 31 - Directory Listing
Modified Tue Aug 2 21:58:18 2011 UTC (4 years, 9 months 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 (4 years, 9 months ago) by gpertea
added SeqAn to tophat source pack

Revision 29 - Directory Listing
Modified Tue Aug 2 21:24:54 2011 UTC (4 years, 9 months ago) by gpertea
adding tophat source work

Revision 28 - Directory Listing
Added Tue Aug 2 21:23:26 2011 UTC (4 years, 9 months ago) by gpertea
adding tophat_cpp dir