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
235 -
Directory Listing
Modified
Mon Apr 23 21:31:55 2012 UTC
(12 years, 4 months ago)
by
gpertea
some clarifications in CIGAR operation parsing
Revision
234 -
Directory Listing
Modified
Wed Apr 11 21:05:36 2012 UTC
(12 years, 4 months ago)
by
gpertea
fixed find_tag() to use the bam_aux_get()
Revision
233 -
Directory Listing
Modified
Wed Apr 11 21:05:01 2012 UTC
(12 years, 4 months ago)
by
gpertea
Revision
232 -
Directory Listing
Modified
Wed Apr 4 18:36:58 2012 UTC
(12 years, 5 months ago)
by
gpertea
Daehwan fixed an egregious bug in find_tag()
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
227 -
Directory Listing
Modified
Mon Mar 26 21:28:07 2012 UTC
(12 years, 5 months ago)
by
gpertea
Revision
226 -
Directory Listing
Modified
Mon Mar 26 21:27:57 2012 UTC
(12 years, 5 months ago)
by
gpertea
Revision
225 -
Directory Listing
Modified
Mon Mar 26 12:07:13 2012 UTC
(12 years, 5 months ago)
by
gpertea
Revision
224 -
Directory Listing
Modified
Mon Mar 26 12:06:25 2012 UTC
(12 years, 5 months ago)
by
gpertea
fixed a silly memory release bug
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
214 -
Directory Listing
Modified
Wed Mar 14 01:47:41 2012 UTC
(12 years, 5 months ago)
by
gpertea
fixed ugly bug in GBamRecord::find_tag()
Revision
213 -
Directory Listing
Modified
Wed Mar 14 01:47:14 2012 UTC
(12 years, 5 months ago)
by
gpertea
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
199 -
Directory Listing
Modified
Mon Mar 5 17:16:24 2012 UTC
(12 years, 6 months ago)
by
gpertea
Revision
198 -
Directory Listing
Modified
Sun Feb 26 18:03:46 2012 UTC
(12 years, 6 months ago)
by
gpertea
Revision
197 -
Directory Listing
Modified
Sun Feb 26 18:02:05 2012 UTC
(12 years, 6 months ago)
by
gpertea
trans.gff3 seems to work
Revision
196 -
Directory Listing
Modified
Fri Feb 24 22:48:54 2012 UTC
(12 years, 6 months ago)
by
gpertea
wip gffread trans-splice
Revision
195 -
Directory Listing
Modified
Thu Feb 23 22:37:36 2012 UTC
(12 years, 6 months ago)
by
gpertea
gff wip
Revision
194 -
Directory Listing
Modified
Tue Feb 21 21:19:11 2012 UTC
(12 years, 6 months ago)
by
gpertea
increased "safe length" for an alignment from 16 to 22
Revision
193 -
Directory Listing
Modified
Fri Feb 17 23:44:04 2012 UTC
(12 years, 6 months ago)
by
gpertea
Revision
192 -
Directory Listing
Modified
Fri Feb 17 23:43:57 2012 UTC
(12 years, 6 months ago)
by
gpertea
Revision
191 -
Directory Listing
Modified
Fri Feb 17 23:33:25 2012 UTC
(12 years, 6 months ago)
by
gpertea
Revision
190 -
Directory Listing
Modified
Fri Feb 17 23:33:17 2012 UTC
(12 years, 6 months ago)
by
gpertea
Revision
189 -
Directory Listing
Modified
Fri Feb 17 23:08:53 2012 UTC
(12 years, 6 months ago)
by
gpertea
added -a option to control the minimum exact adaptor match to be trimmed at the ends
Revision
188 -
Directory Listing
Modified
Fri Feb 17 05:42:37 2012 UTC
(12 years, 6 months ago)
by
gpertea
fqtrim works
Revision
187 -
Directory Listing
Modified
Fri Feb 17 05:42:21 2012 UTC
(12 years, 6 months ago)
by
gpertea
fqtrim
Revision
186 -
Directory Listing
Modified
Thu Feb 16 22:15:58 2012 UTC
(12 years, 6 months ago)
by
gpertea
adjust safelen threshold from 12 to 16
Revision
185 -
Directory Listing
Modified
Thu Feb 16 22:05:42 2012 UTC
(12 years, 6 months ago)
by
gpertea
Revision
184 -
Directory Listing
Modified
Thu Feb 16 21:59:44 2012 UTC
(12 years, 6 months ago)
by
gpertea
works
Revision
183 -
Directory Listing
Modified
Thu Feb 16 21:59:33 2012 UTC
(12 years, 6 months ago)
by
gpertea
works
Revision
182 -
Directory Listing
Modified
Thu Feb 16 21:33:27 2012 UTC
(12 years, 6 months ago)
by
gpertea
Revision
181 -
Directory Listing
Modified
Thu Feb 16 21:24:29 2012 UTC
(12 years, 6 months ago)
by
gpertea
fqtrim works
Revision
180 -
Directory Listing
Modified
Thu Feb 16 21:24:04 2012 UTC
(12 years, 6 months ago)
by
gpertea
works probably
Revision
179 -
Directory Listing
Modified
Thu Feb 16 16:23:45 2012 UTC
(12 years, 6 months ago)
by
gpertea
moved bit handling inlines from GBase to GBitVec
Revision
178 -
Directory Listing
Modified
Thu Feb 16 07:10:45 2012 UTC
(12 years, 6 months ago)
by
gpertea
fqtrim
Revision
177 -
Directory Listing
Modified
Thu Feb 16 07:10:32 2012 UTC
(12 years, 6 months ago)
by
gpertea
collectSeeds unified
Revision
176 -
Directory Listing
Modified
Thu Feb 16 03:47:16 2012 UTC
(12 years, 6 months ago)
by
gpertea
fqtrim reworked
Revision
175 -
Directory Listing
Modified
Thu Feb 16 03:46:59 2012 UTC
(12 years, 6 months ago)
by
gpertea
Revision
174 -
Directory Listing
Modified
Wed Feb 15 21:04:38 2012 UTC
(12 years, 6 months ago)
by
gpertea
wip fqtrim
Revision
173 -
Directory Listing
Modified
Wed Feb 15 03:34:29 2012 UTC
(12 years, 6 months ago)
by
gpertea
wip fqtrim
Revision
172 -
Directory Listing
Modified
Wed Feb 15 03:33:40 2012 UTC
(12 years, 6 months ago)
by
gpertea
wip fqtrim
Revision
171 -
Directory Listing
Modified
Tue Feb 14 22:36:26 2012 UTC
(12 years, 6 months ago)
by
gpertea
wip fqtrim
Revision
170 -
Directory Listing
Modified
Tue Feb 14 22:35:51 2012 UTC
(12 years, 6 months ago)
by
gpertea
wip fqtrim
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
162 -
Directory Listing
Modified
Tue Feb 7 19:27:55 2012 UTC
(12 years, 6 months ago)
by
gpertea
initial map_report commit
Revision
161 -
Directory Listing
Modified
Tue Feb 7 19:27:04 2012 UTC
(12 years, 6 months ago)
by
gpertea
adding map_report (raw counts cuffdiff)
Revision
160 -
Directory Listing
Modified
Fri Feb 3 15:31:57 2012 UTC
(12 years, 7 months ago)
by
gpertea
added fq_extract script
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
156 -
Directory Listing
Modified
Fri Jan 27 18:29:55 2012 UTC
(12 years, 7 months ago)
by
gpertea
adding refactored TinyThread++ code
Revision
155 -
Directory Listing
Modified
Wed Jan 25 21:06:46 2012 UTC
(12 years, 7 months ago)
by
gpertea
fix for a subtle XLocus building bug
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
153 -
Directory Listing
Modified
Fri Jan 20 22:35:32 2012 UTC
(12 years, 7 months ago)
by
gpertea
still working on trans-splicing/fusions in gff
Revision
152 -
Directory Listing
Modified
Fri Jan 13 23:08:23 2012 UTC
(12 years, 7 months ago)
by
gpertea
wip
Revision
151 -
Directory Listing
Modified
Fri Jan 13 22:56:48 2012 UTC
(12 years, 7 months ago)
by
gpertea
wip: trans-spliced and fusion transcripts
Revision
150 -
Directory Listing
Modified
Fri Jan 13 17:20:39 2012 UTC
(12 years, 7 months ago)
by
gpertea
fixed parsing bug for extractAttr();
Gstrcmp() and Gstricmp() take a 3rd optional param to make them work like strncmp()
Revision
149 -
Directory Listing
Modified
Fri Jan 13 17:18:27 2012 UTC
(12 years, 7 months ago)
by
gpertea
fixed crash when given input file is '-'
Revision
148 -
Directory Listing
Modified
Thu Dec 22 21:02:45 2011 UTC
(12 years, 8 months ago)
by
gpertea
added mblasm sources
Revision
147 -
Directory Listing
Modified
Thu Dec 22 21:01:52 2011 UTC
(12 years, 8 months ago)
by
gpertea
adding my old mgblast assembler
Revision
146 -
Directory Listing
Modified
Thu Dec 22 20:41:43 2011 UTC
(12 years, 8 months ago)
by
gpertea
removed useless operator>
Revision
145 -
Directory Listing
Modified
Thu Dec 22 19:19:10 2011 UTC
(12 years, 8 months ago)
by
gpertea
Revision
144 -
Directory Listing
Modified
Thu Dec 22 19:15:46 2011 UTC
(12 years, 8 months ago)
by
gpertea
added GBitVec.h; removed operator> requirement for sorted vectors; swap() is now template Gswap()
Revision
143 -
Directory Listing
Modified
Thu Dec 22 19:14:29 2011 UTC
(12 years, 8 months ago)
by
gpertea
removed useless operator>
Revision
142 -
Directory Listing
Modified
Thu Dec 22 19:11:36 2011 UTC
(12 years, 8 months ago)
by
gpertea
removed useless operator>
Revision
141 -
Directory Listing
Modified
Thu Dec 22 19:11:20 2011 UTC
(12 years, 8 months ago)
by
gpertea
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
136 -
Directory Listing
Modified
Tue Dec 13 16:18:24 2011 UTC
(12 years, 8 months ago)
by
gpertea
added my mobile fput/fget scripts
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
134 -
Directory Listing
Modified
Fri Dec 9 17:52:20 2011 UTC
(12 years, 8 months ago)
by
gpertea
Revision
133 -
Directory Listing
Modified
Fri Dec 9 15:59:14 2011 UTC
(12 years, 8 months ago)
by
gpertea
TODO: detect sam/bam input for samopen
Revision
132 -
Directory Listing
Modified
Thu Dec 8 02:53:32 2011 UTC
(12 years, 8 months ago)
by
gpertea
GBam working; fixed serious memory leak in GVec::setCapacity()
Revision
131 -
Directory Listing
Modified
Thu Dec 8 02:53:00 2011 UTC
(12 years, 8 months ago)
by
gpertea
working
Revision
130 -
Directory Listing
Modified
Thu Dec 8 01:18:08 2011 UTC
(12 years, 8 months ago)
by
gpertea
fixed exon positions
Revision
129 -
Directory Listing
Modified
Wed Dec 7 20:59:43 2011 UTC
(12 years, 8 months ago)
by
gpertea
Revision
128 -
Directory Listing
Modified
Wed Dec 7 20:47:58 2011 UTC
(12 years, 8 months ago)
by
gpertea
wip
Revision
127 -
Directory Listing
Modified
Wed Dec 7 18:31:56 2011 UTC
(12 years, 8 months ago)
by
gpertea
Revision
126 -
Directory Listing
Modified
Tue Dec 6 22:45:06 2011 UTC
(12 years, 8 months ago)
by
gpertea
wip
Revision
125 -
Directory Listing
Modified
Tue Dec 6 19:22:50 2011 UTC
(12 years, 8 months ago)
by
gpertea
minor stats formatting
Revision
124 -
Directory Listing
Modified
Tue Dec 6 04:54:35 2011 UTC
(12 years, 8 months ago)
by
gpertea
GBam wip
Revision
123 -
Directory Listing
Modified
Mon Dec 5 22:21:21 2011 UTC
(12 years, 8 months ago)
by
gpertea
bamread files
Revision
122 -
Directory Listing
Modified
Mon Dec 5 22:19:59 2011 UTC
(12 years, 8 months ago)
by
gpertea
bamread project for testing GBam classes
Revision
121 -
Directory Listing
Modified
Mon Dec 5 22:18:48 2011 UTC
(12 years, 8 months ago)
by
gpertea
added GBam BAM reader/writer classes (wip)
Revision
120 -
Directory Listing
Modified
Sun Dec 4 01:46:51 2011 UTC
(12 years, 9 months ago)
by
gpertea
Revision
119 -
Directory Listing
Modified
Sun Dec 4 01:46:18 2011 UTC
(12 years, 9 months ago)
by
gpertea
fixed calculation of Sn for locus
Revision
118 -
Directory Listing
Modified
Sun Nov 27 21:14:57 2011 UTC
(12 years, 9 months ago)
by
gpertea
fix locus Sn calculation
Revision
117 -
Directory Listing
Modified
Wed Nov 23 21:27:59 2011 UTC
(12 years, 9 months ago)
by
gpertea
gbs2gff fixes
Revision
116 -
Directory Listing
Modified
Mon Nov 7 21:25:56 2011 UTC
(12 years, 9 months ago)
by
gpertea
Ensembl conversion corrections
Revision
115 -
Directory Listing
Modified
Mon Nov 7 21:25:03 2011 UTC
(12 years, 9 months ago)
by
gpertea
fixed horrendous bug in GList.hh (resizing GVec)
Revision
114 -
Directory Listing
Modified
Mon Nov 7 15:15:11 2011 UTC
(12 years, 9 months ago)
by
gpertea
backup scripts updated
Revision
113 -
Directory Listing
Modified
Mon Nov 7 13:24:06 2011 UTC
(12 years, 9 months ago)
by
gpertea
gb2gff tweaks
Revision
112 -
Directory Listing
Modified
Tue Nov 1 20:57:08 2011 UTC
(12 years, 10 months ago)
by
gpertea
added backup scripts, improved conversion for NCBI human annotation
Revision
111 -
Directory Listing
Modified
Tue Oct 25 17:05:09 2011 UTC
(12 years, 10 months ago)
by
gpertea
wip
Revision
110 -
Directory Listing
Modified
Wed Oct 12 17:17:00 2011 UTC
(12 years, 10 months ago)
by
gpertea
minor script updates
Revision
109 -
Directory Listing
Modified
Tue Oct 11 19:50:14 2011 UTC
(12 years, 10 months ago)
by
gpertea
added GStr::reverse(), GAlnExtend stringency tweaks
Revision
108 -
Directory Listing
Modified
Tue Oct 11 19:49:29 2011 UTC
(12 years, 10 months ago)
by
gpertea
made more stringent on the 5' end, other tests and fixes
Revision
107 -
Directory Listing
Modified
Tue Oct 11 12:31:50 2011 UTC
(12 years, 10 months ago)
by
gpertea
wip GYarn (threads)
Revision
106 -
Directory Listing
Modified
Mon Oct 10 21:45:05 2011 UTC
(12 years, 10 months ago)
by
gpertea
Revision
105 -
Directory Listing
Modified
Mon Oct 10 21:44:55 2011 UTC
(12 years, 10 months ago)
by
gpertea
wip - works?
Revision
104 -
Directory Listing
Modified
Mon Oct 10 19:34:20 2011 UTC
(12 years, 10 months ago)
by
gpertea
fixed GVec, GArray to use new[] instead of malloc
Revision
103 -
Directory Listing
Modified
Mon Oct 10 19:33:39 2011 UTC
(12 years, 10 months ago)
by
gpertea
wip
Revision
102 -
Directory Listing
Modified
Fri Oct 7 21:44:59 2011 UTC
(12 years, 10 months ago)
by
gpertea
wip
Revision
101 -
Directory Listing
Modified
Fri Oct 7 21:13:55 2011 UTC
(12 years, 10 months ago)
by
gpertea
adjusting params
Revision
100 -
Directory Listing
Modified
Fri Oct 7 21:13:33 2011 UTC
(12 years, 10 months ago)
by
gpertea
adjusting params
Revision
99 -
Directory Listing
Modified
Thu Oct 6 20:49:17 2011 UTC
(12 years, 10 months ago)
by
gpertea
wip
Revision
98 -
Directory Listing
Modified
Thu Oct 6 20:49:00 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
96 -
Directory Listing
Modified
Wed Oct 5 18:31:48 2011 UTC
(12 years, 11 months ago)
by
gpertea
moved match_LeftEnd() and match_RightEnd() to GAlnExtend
Revision
95 -
Directory Listing
Modified
Wed Oct 5 18:30:51 2011 UTC
(12 years, 11 months ago)
by
gpertea
Revision
94 -
Directory Listing
Modified
Tue Oct 4 21:27:35 2011 UTC
(12 years, 11 months ago)
by
gpertea
wip
Revision
93 -
Directory Listing
Modified
Tue Oct 4 12:27:31 2011 UTC
(12 years, 11 months ago)
by
gpertea
added gapped alignment extension code
Revision
92 -
Directory Listing
Modified
Mon Oct 3 21:36:42 2011 UTC
(12 years, 11 months ago)
by
gpertea
switching to gclib/GAlnExtend
Revision
91 -
Directory Listing
Modified
Mon Oct 3 20:51:09 2011 UTC
(12 years, 11 months ago)
by
gpertea
extended 'x' code to also include interleaved exons on opposite strand
Revision
90 -
Directory Listing
Modified
Mon Oct 3 18:45:22 2011 UTC
(12 years, 11 months ago)
by
gpertea
reverseChars() minor edit
Revision
89 -
Directory Listing
Modified
Mon Oct 3 18:42:24 2011 UTC
(12 years, 11 months ago)
by
gpertea
separate wrappers for 5' and 3' alignments
Revision
88 -
Directory Listing
Modified
Mon Oct 3 16:34:03 2011 UTC
(12 years, 11 months ago)
by
gpertea
starting to add polyA/T trimming
Revision
87 -
Directory Listing
Modified
Sun Oct 2 19:12:03 2011 UTC
(12 years, 11 months ago)
by
gpertea
disable pointer arithmetic in GXGreedyExtend(), it's bad
Revision
86 -
Directory Listing
Modified
Fri Sep 30 21:38:39 2011 UTC
(12 years, 11 months ago)
by
gpertea
fixed a few more subtle bugs
Revision
85 -
Directory Listing
Modified
Fri Sep 30 20:38:13 2011 UTC
(12 years, 11 months ago)
by
gpertea
rewrote, set params X=8, M=2, N=3
Revision
84 -
Directory Listing
Modified
Fri Sep 30 03:19:32 2011 UTC
(12 years, 11 months ago)
by
gpertea
wip bad
Revision
83 -
Directory Listing
Modified
Thu Sep 29 21:32:42 2011 UTC
(12 years, 11 months ago)
by
gpertea
wip
Revision
82 -
Directory Listing
Modified
Thu Sep 29 20:46:39 2011 UTC
(12 years, 11 months ago)
by
gpertea
wip
Revision
81 -
Directory Listing
Modified
Thu Sep 29 19:02:24 2011 UTC
(12 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
(12 years, 11 months ago)
by
gpertea
wip
Revision
79 -
Directory Listing
Modified
Wed Sep 28 19:54:42 2011 UTC
(12 years, 11 months ago)
by
gpertea
wip, fixed memory leaks
Revision
78 -
Directory Listing
Modified
Wed Sep 28 03:20:10 2011 UTC
(12 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
(12 years, 11 months ago)
by
gpertea
wip - cutting seeds, finalize()
Revision
76 -
Directory Listing
Modified
Tue Sep 27 12:37:02 2011 UTC
(12 years, 11 months ago)
by
gpertea
u
Revision
75 -
Directory Listing
Modified
Tue Sep 27 02:24:57 2011 UTC
(12 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
(12 years, 11 months ago)
by
gpertea
added seqalign files
Revision
73 -
Directory Listing
Modified
Tue Sep 27 01:20:53 2011 UTC
(12 years, 11 months ago)
by
gpertea
creating seqalign storage
Revision
72 -
Directory Listing
Modified
Tue Sep 27 01:20:21 2011 UTC
(12 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
(12 years, 11 months ago)
by
gpertea
gridx fixed to export PERL5LIB and PYTHONPATH
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
66 -
Directory Listing
Modified
Fri Sep 16 18:33:54 2011 UTC
(12 years, 11 months ago)
by
gpertea
made some Flybase GFF3 "errors" non-fatal
Revision
65 -
Directory Listing
Modified
Fri Sep 16 18:33:19 2011 UTC
(12 years, 11 months ago)
by
gpertea
Revision
64 -
Directory Listing
Modified
Fri Sep 9 20:58:16 2011 UTC
(12 years, 11 months 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
(12 years, 11 months ago)
by
gpertea
Revision
62 -
Directory Listing
Modified
Fri Sep 9 20:19:10 2011 UTC
(12 years, 11 months ago)
by
gpertea
added --force-exons option to force "exon" subfeatures
Revision
61 -
Directory Listing
Modified
Fri Sep 9 18:46:01 2011 UTC
(12 years, 11 months ago)
by
gpertea
removed startChanged flag, not needed
Revision
60 -
Directory Listing
Modified
Fri Sep 9 18:00:55 2011 UTC
(12 years, 11 months 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
(12 years, 11 months ago)
by
gpertea
finally fixed the placeGf clustering bug
Revision
58 -
Directory Listing
Modified
Fri Sep 9 14:01:30 2011 UTC
(12 years, 11 months 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
(12 years, 11 months ago)
by
gpertea
wip
Revision
56 -
Directory Listing
Modified
Thu Sep 8 05:47:09 2011 UTC
(12 years, 11 months ago)
by
gpertea
RPS20P29, ENSG00000241828 not collapsing
Revision
55 -
Directory Listing
Modified
Thu Sep 8 05:46:53 2011 UTC
(12 years, 11 months ago)
by
gpertea
RPS20P29, ENSG00000241828 not collapsing
Revision
54 -
Directory Listing
Modified
Thu Sep 8 05:46:16 2011 UTC
(12 years, 11 months ago)
by
gpertea
debug RPS20P29 ENSG00000241828 not collapsing
Revision
53 -
Directory Listing
Modified
Thu Sep 8 02:43:56 2011 UTC
(12 years, 11 months ago)
by
gpertea
Revision
52 -
Directory Listing
Modified
Thu Sep 8 02:43:30 2011 UTC
(12 years, 11 months 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
(12 years, 11 months 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
(12 years, 11 months 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
(12 years, 11 months ago)
by
gpertea
minor edits
Revision
48 -
Directory Listing
Modified
Wed Sep 7 16:07:32 2011 UTC
(12 years, 11 months ago)
by
gpertea
longest CDS is now kept on -MK containment
Revision
47 -
Directory Listing
Modified
Wed Sep 7 01:12:20 2011 UTC
(12 years, 11 months 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
(12 years, 11 months ago)
by
gpertea
fixed GStr[-2] bug
Revision
45 -
Directory Listing
Modified
Tue Sep 6 18:19:20 2011 UTC
(12 years, 11 months ago)
by
gpertea
added gfview files
Revision
44 -
Directory Listing
Modified
Tue Sep 6 18:15:55 2011 UTC
(12 years, 11 months ago)
by
gpertea
added gfview
Revision
43 -
Directory Listing
Modified
Tue Sep 6 17:41:50 2011 UTC
(12 years, 11 months ago)
by
gpertea
m
Revision
42 -
Directory Listing
Modified
Tue Sep 6 17:40:45 2011 UTC
(12 years, 11 months ago)
by
gpertea
minor edit
Revision
41 -
Directory Listing
Modified
Sat Aug 27 16:58:00 2011 UTC
(13 years ago)
by
gpertea
added fix for fileExists() under MSVC
Revision
40 -
Directory Listing
Modified
Sat Aug 27 16:48:50 2011 UTC
(13 years ago)
by
gpertea
added clview files and examples
Revision
39 -
Directory Listing
Modified
Sat Aug 27 15:50:52 2011 UTC
(13 years ago)
by
gpertea
clview added
Revision
38 -
Directory Listing
Modified
Sat Aug 27 15:42:15 2011 UTC
(13 years ago)
by
gpertea
Revision
37 -
Directory Listing
Modified
Mon Aug 22 16:17:34 2011 UTC
(13 years ago)
by
gpertea
wip
Revision
36 -
Directory Listing
Modified
Mon Aug 22 15:56:21 2011 UTC
(13 years ago)
by
gpertea
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
Modified
Tue Aug 2 21:23:26 2011 UTC
(13 years, 1 month ago)
by
gpertea
adding tophat_cpp dir
Revision
27 -
Directory Listing
Modified
Wed Jul 27 20:43:37 2011 UTC
(13 years, 1 month ago)
by
gpertea
Revision
26 -
Directory Listing
Modified
Wed Jul 27 19:39:27 2011 UTC
(13 years, 1 month ago)
by
gpertea
added missing gff_utils source
Revision
25 -
Directory Listing
Modified
Tue Jul 26 21:50:53 2011 UTC
(13 years, 1 month ago)
by
gpertea
Revision
24 -
Directory Listing
Modified
Tue Jul 26 21:46:39 2011 UTC
(13 years, 1 month ago)
by
gpertea
Revision
23 -
Directory Listing
Modified
Tue Jul 26 21:44:38 2011 UTC
(13 years, 1 month ago)
by
gpertea
adding misc scripts
Revision
22 -
Directory Listing
Modified
Tue Jul 26 21:43:45 2011 UTC
(13 years, 1 month ago)
by
gpertea
various scripts
Revision
21 -
Directory Listing
Modified
Mon Jul 18 22:35:05 2011 UTC
(13 years, 1 month 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
(13 years, 1 month ago)
by
gpertea
added cuffcompare sources
Revision
19 -
Directory Listing
Modified
Mon Jul 18 21:07:43 2011 UTC
(13 years, 1 month ago)
by
gpertea
mkdir cuffcompare
Revision
18 -
Directory Listing
Modified
Mon Jul 18 21:00:21 2011 UTC
(13 years, 1 month ago)
by
gpertea
added a few more source files, test code
Revision
17 -
Directory Listing
Modified
Mon Jul 18 20:57:05 2011 UTC
(13 years, 1 month ago)
by
gpertea
sync with local source
Revision
16 -
Directory Listing
Modified
Mon Jul 18 20:56:02 2011 UTC
(13 years, 1 month ago)
by
gpertea
sync with local source
Revision
15 -
Directory Listing
Modified
Mon Jul 18 20:53:45 2011 UTC
(13 years, 1 month ago)
by
gpertea
sync with local src
Revision
14 -
Directory Listing
Modified
Mon Jul 18 20:36:48 2011 UTC
(13 years, 1 month ago)
by
gpertea
added old trimpoly code just for archive
Revision
13 -
Directory Listing
Modified
Mon Jul 18 20:35:43 2011 UTC
(13 years, 1 month ago)
by
gpertea
sync with my local source
Revision
12 -
Directory Listing
Modified
Wed Jan 26 19:05:05 2011 UTC
(13 years, 7 months ago)
by
gpertea
added qv-threshold trimming
Revision
11 -
Directory Listing
Modified
Tue Mar 23 18:03:12 2010 UTC
(14 years, 5 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
(14 years, 5 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
(14 years, 5 months ago)
by
gpertea
fixed bug causing overtrimming
Revision
8 -
Directory Listing
Modified
Mon Mar 22 22:11:25 2010 UTC
(14 years, 5 months ago)
by
gpertea
added cdbfasta source files
Revision
7 -
Directory Listing
Modified
Mon Mar 22 22:08:51 2010 UTC
(14 years, 5 months ago)
by
gpertea
mkdir cdbfasta
Revision
6 -
Directory Listing
Modified
Mon Mar 22 22:07:27 2010 UTC
(14 years, 5 months ago)
by
gpertea
added gffread sources
Revision
5 -
Directory Listing
Modified
Mon Mar 22 22:06:27 2010 UTC
(14 years, 5 months ago)
by
gpertea
mkdir gffread
Revision
4 -
Directory Listing
Modified
Mon Mar 22 22:05:23 2010 UTC
(14 years, 5 months ago)
by
gpertea
initial commit
Revision
3 -
Directory Listing
Modified
Mon Mar 22 22:04:34 2010 UTC
(14 years, 5 months ago)
by
gpertea
mkdir
Revision
2 -
Directory Listing
Modified
Mon Mar 22 22:03:27 2010 UTC
(14 years, 5 months ago)
by
gpertea
added my gclib source files
Revision
1 -
Directory Listing
Added
Mon Mar 22 22:01:50 2010 UTC
(14 years, 5 months ago)
by
gpertea
import