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Revision 310 - Directory Listing
Modified Fri Mar 22 20:06:27 2013 UTC (2 years, 10 months ago) by gpertea
sync with igm repo

Revision 309 - Directory Listing
Modified Fri Mar 22 19:47:48 2013 UTC (2 years, 10 months ago) by gpertea
fixed -J crash

Revision 308 - Directory Listing
Modified Wed Feb 27 17:09:40 2013 UTC (2 years, 11 months ago) by gpertea
added fqsort etc.

Revision 307 - Directory Listing
Modified Thu Feb 21 18:44:52 2013 UTC (2 years, 11 months ago) by gpertea
mingw debugging now possible in eclipse (no symbol stripping)

Revision 306 - Directory Listing
Modified Thu Feb 21 18:42:33 2013 UTC (2 years, 11 months ago) by gpertea

Revision 305 - Directory Listing
Modified Tue Jan 15 22:54:32 2013 UTC (3 years ago) by gpertea
some updated scripts

Revision 304 - Directory Listing
Modified Tue Nov 20 17:47:37 2012 UTC (3 years, 2 months ago) by gpertea
modifying to include range selection/display

Revision 303 - Directory Listing
Modified Fri Oct 26 17:29:47 2012 UTC (3 years, 3 months ago) by gpertea
fix out of sync with igm

Revision 302 - Directory Listing
Modified Fri Oct 26 12:45:36 2012 UTC (3 years, 3 months ago) by gpertea
process_read implemented


Revision 301 - Directory Listing
Modified Fri Oct 26 12:44:32 2012 UTC (3 years, 3 months ago) by gpertea
minor refactoring


Revision 300 - Directory Listing
Modified Wed Oct 24 22:40:48 2012 UTC (3 years, 3 months ago) by gpertea

Revision 299 - Directory Listing
Modified Wed Oct 24 22:40:33 2012 UTC (3 years, 3 months ago) by gpertea
wip

Revision 298 - Directory Listing
Modified Tue Oct 23 02:50:26 2012 UTC (3 years, 3 months ago) by gpertea
wip

Revision 297 - Directory Listing
Modified Tue Oct 23 01:00:17 2012 UTC (3 years, 3 months ago) by gpertea
reformatting a bit

Revision 296 - Directory Listing
Modified Mon Oct 22 19:03:47 2012 UTC (3 years, 3 months ago) by gpertea

Revision 295 - Directory Listing
Modified Mon Oct 22 19:01:32 2012 UTC (3 years, 3 months ago) by gpertea
minor GVec change to Add() function

Revision 294 - Directory Listing
Modified Mon Oct 22 18:59:56 2012 UTC (3 years, 3 months ago) by gpertea
added -O option to only output affected reads

Revision 293 - Directory Listing
Modified Sun Oct 21 21:03:18 2012 UTC (3 years, 3 months ago) by gpertea
wip

Revision 292 - Directory Listing
Modified Sun Oct 21 18:00:08 2012 UTC (3 years, 3 months ago) by gpertea

Revision 291 - Directory Listing
Modified Sun Oct 21 17:48:22 2012 UTC (3 years, 3 months ago) by gpertea
renaming rejoin to stringtie

Revision 290 - Directory Listing
Modified Wed Oct 17 19:24:59 2012 UTC (3 years, 3 months ago) by gpertea

Revision 289 - Directory Listing
Modified Tue Oct 16 21:04:14 2012 UTC (3 years, 3 months ago) by gpertea

Revision 288 - Directory Listing
Modified Tue Oct 16 14:45:03 2012 UTC (3 years, 3 months ago) by gpertea
wip

Revision 287 - Directory Listing
Modified Mon Oct 15 18:37:20 2012 UTC (3 years, 3 months ago) by gpertea

Revision 286 - Directory Listing
Modified Mon Oct 15 17:31:47 2012 UTC (3 years, 3 months ago) by gpertea
slight mods for rejoin use

Revision 285 - Directory Listing
Modified Mon Oct 15 17:31:30 2012 UTC (3 years, 3 months ago) by gpertea
wip

Revision 284 - Directory Listing
Modified Mon Oct 15 14:02:35 2012 UTC (3 years, 3 months ago) by gpertea

Revision 283 - Directory Listing
Modified Fri Oct 12 21:39:24 2012 UTC (3 years, 4 months ago) by gpertea
working on rejoin

Revision 282 - Directory Listing
Modified Fri Oct 12 18:48:38 2012 UTC (3 years, 4 months ago) by gpertea

Revision 281 - Directory Listing
Modified Tue Oct 9 23:26:59 2012 UTC (3 years, 4 months ago) by gpertea

Revision 280 - Directory Listing
Modified Mon Oct 8 21:31:38 2012 UTC (3 years, 4 months ago) by gpertea

Revision 279 - Directory Listing
Modified Mon Oct 8 19:51:07 2012 UTC (3 years, 4 months ago) by gpertea
added my svn scripts

Revision 278 - Directory Listing
Modified Mon Oct 8 19:44:47 2012 UTC (3 years, 4 months ago) by gpertea
rejoin - added files

Revision 277 - Directory Listing
Modified Mon Oct 8 19:43:48 2012 UTC (3 years, 4 months ago) by gpertea
adding Ela's RNA-Seq assembler

Revision 276 - Directory Listing
Modified Mon Oct 8 16:16:54 2012 UTC (3 years, 4 months ago) by gpertea

Revision 275 - Directory Listing
Modified Mon Oct 8 14:23:56 2012 UTC (3 years, 4 months ago) by gpertea
-a should still add the "full tokens"

Revision 274 - Directory Listing
Modified Sun Oct 7 01:42:09 2012 UTC (3 years, 4 months ago) by gpertea

Revision 273 - Directory Listing
Modified Sun Oct 7 01:35:55 2012 UTC (3 years, 4 months ago) by gpertea
cdbfasta -a now only indexes the accessions (not the full token); -n option 
used with -a now specifies how many accessions per defline to key in

Revision 272 - Directory Listing
Modified Fri Oct 5 16:52:37 2012 UTC (3 years, 4 months ago) by gpertea

Revision 271 - Directory Listing
Modified Fri Oct 5 16:51:56 2012 UTC (3 years, 4 months ago) by gpertea
various updates to UniProt protocol

Revision 270 - Directory Listing
Modified Thu Oct 4 23:03:44 2012 UTC (3 years, 4 months ago) by gpertea
finally zooming/layout scrollbar updates are fixed in v1.7

Revision 269 - Directory Listing
Modified Thu Oct 4 16:30:23 2012 UTC (3 years, 4 months ago) by gpertea
fixed scrypt/sdecrypt in dbSession.pm 

Revision 268 - Directory Listing
Modified Thu Oct 4 14:04:46 2012 UTC (3 years, 4 months ago) by gpertea

Revision 267 - Directory Listing
Modified Thu Oct 4 14:04:26 2012 UTC (3 years, 4 months ago) by gpertea
modified for Fox 1.7 - still working on "resize" notification

Revision 266 - Directory Listing
Modified Tue Sep 11 21:53:47 2012 UTC (3 years, 5 months ago) by gpertea
fixed a stats bug counting matching i-chains multiple times

Revision 265 - Directory Listing
Modified Mon Aug 27 18:21:44 2012 UTC (3 years, 5 months ago) by gpertea
minor fixes by codan and gcc 4.7

Revision 264 - Directory Listing
Modified Mon Aug 27 18:21:11 2012 UTC (3 years, 5 months ago) by gpertea
minor refactoring etc

Revision 263 - Directory Listing
Modified Mon Jul 30 21:38:58 2012 UTC (3 years, 6 months ago) by gpertea
resuming works

Revision 262 - Directory Listing
Modified Wed Jul 25 20:29:58 2012 UTC (3 years, 6 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, 6 months ago) by gpertea

Revision 260 - Directory Listing
Modified Tue Jul 24 20:10:50 2012 UTC (3 years, 6 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, 7 months ago) by gpertea
updated to v2.0.4

Revision 258 - Directory Listing
Modified Tue Jun 26 22:29:50 2012 UTC (3 years, 7 months ago) by gpertea
commented out saprintf(), not used

Revision 257 - Directory Listing
Modified Mon Jun 18 21:08:57 2012 UTC (3 years, 7 months ago) by gpertea
update

Revision 256 - Directory Listing
Modified Mon Jun 11 19:35:44 2012 UTC (3 years, 8 months ago) by gpertea
sync with Daehwan's fixes

Revision 255 - Directory Listing
Modified Mon Jun 4 20:02:45 2012 UTC (3 years, 8 months ago) by gpertea
minor reformatting by Cole

Revision 254 - Directory Listing
Modified Wed May 30 22:29:09 2012 UTC (3 years, 8 months ago) by gpertea
fix_map_ordering wip to throw away not "acceptable" mappings

Revision 253 - Directory Listing
Modified Tue May 29 15:21:30 2012 UTC (3 years, 8 months ago) by gpertea
fixed a fatal bug with exons.First() being accessed even when exons.Count() is 0

Revision 252 - Directory Listing
Modified Sat May 26 00:55:09 2012 UTC (3 years, 8 months ago) by gpertea
Interval tree updates, wip Store/Load

Revision 251 - Directory Listing
Modified Thu May 24 22:47:01 2012 UTC (3 years, 8 months ago) by gpertea

Revision 250 - Directory Listing
Modified Thu May 24 18:21:10 2012 UTC (3 years, 8 months ago) by gpertea
added generic storage function type; wip serialization for GIntervalTree

Revision 249 - Directory Listing
Modified Wed May 23 22:35:38 2012 UTC (3 years, 8 months ago) by gpertea
moved sorting into GVec.hh

Revision 248 - Directory Listing
Modified Wed May 23 22:10:55 2012 UTC (3 years, 8 months ago) by gpertea
put GVec and GPVec in GVec.hh, added GIntervalTree.hh

Revision 247 - Directory Listing
Modified Thu May 17 03:37:32 2012 UTC (3 years, 8 months ago) by gpertea
fixed the prefilter bug, I think

Revision 246 - Directory Listing
Modified Wed May 16 22:42:35 2012 UTC (3 years, 8 months ago) by gpertea
wip, -M option still broken!

Revision 245 - Directory Listing
Modified Wed May 16 21:51:01 2012 UTC (3 years, 8 months ago) by gpertea
merge-sync attempt

Revision 244 - Directory Listing
Modified Wed May 16 20:38:28 2012 UTC (3 years, 8 months ago) by gpertea
seems to work, before sync

Revision 243 - Directory Listing
Modified Wed May 16 16:41:58 2012 UTC (3 years, 8 months ago) by gpertea
wip prep_reads

Revision 242 - Directory Listing
Modified Tue May 15 21:37:24 2012 UTC (3 years, 8 months ago) by gpertea
wip!!!

Revision 241 - Directory Listing
Modified Tue May 15 01:44:51 2012 UTC (3 years, 9 months ago) by gpertea
wip tophat

Revision 240 - Directory Listing
Modified Mon May 14 21:35:52 2012 UTC (3 years, 9 months ago) by gpertea
wip tophat accepted_hits

Revision 239 - Directory Listing
Modified Mon May 14 21:01:08 2012 UTC (3 years, 9 months ago) by gpertea
wip prep_reads.cpp, tophat

Revision 238 - Directory Listing
Modified Wed May 9 12:14:58 2012 UTC (3 years, 9 months ago) by gpertea
wip

Revision 237 - Directory Listing
Modified Mon May 7 23:30:42 2012 UTC (3 years, 9 months ago) by gpertea
wip

Revision 236 - Directory Listing
Modified Fri May 4 22:20:02 2012 UTC (3 years, 9 months ago) by gpertea
sync, wip prep_reads

Revision 235 - Directory Listing
Modified Mon Apr 23 21:31:55 2012 UTC (3 years, 9 months ago) by gpertea
some clarifications in CIGAR operation parsing

Revision 234 - Directory Listing
Modified Wed Apr 11 21:05:36 2012 UTC (3 years, 10 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 (3 years, 10 months ago) by gpertea

Revision 232 - Directory Listing
Modified Wed Apr 4 18:36:58 2012 UTC (3 years, 10 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 (3 years, 10 months ago) by gpertea
resync

Revision 230 - Directory Listing
Modified Thu Mar 29 21:44:57 2012 UTC (3 years, 10 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 (3 years, 10 months ago) by gpertea
prefiltering seems to work

Revision 228 - Directory Listing
Modified Wed Mar 28 05:13:28 2012 UTC (3 years, 10 months ago) by gpertea
wip - prefiltering fix

Revision 227 - Directory Listing
Modified Mon Mar 26 21:28:07 2012 UTC (3 years, 10 months ago) by gpertea

Revision 226 - Directory Listing
Modified Mon Mar 26 21:27:57 2012 UTC (3 years, 10 months ago) by gpertea

Revision 225 - Directory Listing
Modified Mon Mar 26 12:07:13 2012 UTC (3 years, 10 months ago) by gpertea

Revision 224 - Directory Listing
Modified Mon Mar 26 12:06:25 2012 UTC (3 years, 10 months ago) by gpertea
fixed a silly memory release bug

Revision 223 - Directory Listing
Modified Fri Mar 23 22:39:52 2012 UTC (3 years, 10 months ago) by gpertea

Revision 222 - Directory Listing
Modified Fri Mar 23 22:39:15 2012 UTC (3 years, 10 months ago) by gpertea

Revision 221 - Directory Listing
Modified Fri Mar 23 03:15:08 2012 UTC (3 years, 10 months ago) by gpertea

Revision 220 - Directory Listing
Modified Thu Mar 22 19:33:00 2012 UTC (3 years, 10 months ago) by gpertea
working, writing rejected.bam

Revision 219 - Directory Listing
Modified Wed Mar 21 21:06:37 2012 UTC (3 years, 10 months ago) by gpertea
almost working with bam all over

Revision 218 - Directory Listing
Modified Tue Mar 20 21:31:57 2012 UTC (3 years, 10 months ago) by gpertea
prep_reads now writes bam

Revision 217 - Directory Listing
Modified Wed Mar 14 19:58:18 2012 UTC (3 years, 11 months ago) by gpertea

Revision 216 - Directory Listing
Modified Wed Mar 14 02:43:25 2012 UTC (3 years, 11 months ago) by gpertea

Revision 215 - Directory Listing
Modified Wed Mar 14 02:06:47 2012 UTC (3 years, 11 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 (3 years, 11 months ago) by gpertea
fixed ugly bug in GBamRecord::find_tag()

Revision 213 - Directory Listing
Modified Wed Mar 14 01:47:14 2012 UTC (3 years, 11 months ago) by gpertea

Revision 212 - Directory Listing
Modified Tue Mar 13 21:32:44 2012 UTC (3 years, 11 months ago) by gpertea
misaligned extra bowtie command fixed

Revision 211 - Directory Listing
Modified Tue Mar 13 21:02:03 2012 UTC (3 years, 11 months ago) by gpertea
wip -- still errors in logs!

Revision 210 - Directory Listing
Modified Tue Mar 13 01:26:20 2012 UTC (3 years, 11 months ago) by gpertea
wip: prep_reads from/to BAM

Revision 209 - Directory Listing
Modified Mon Mar 12 23:24:11 2012 UTC (3 years, 11 months ago) by gpertea

Revision 208 - Directory Listing
Modified Mon Mar 12 23:11:55 2012 UTC (3 years, 11 months ago) by gpertea
removed symlink

Revision 207 - Directory Listing
Modified Mon Mar 12 21:39:30 2012 UTC (3 years, 11 months ago) by gpertea
wip 

Revision 206 - Directory Listing
Modified Mon Mar 12 18:02:35 2012 UTC (3 years, 11 months ago) by gpertea
updated

Revision 205 - Directory Listing
Modified Mon Mar 12 17:40:44 2012 UTC (3 years, 11 months ago) by gpertea
silly bug fix

Revision 204 - Directory Listing
Modified Mon Mar 12 15:51:21 2012 UTC (3 years, 11 months ago) by gpertea
more fixes for bam2fastx.cpp

Revision 203 - Directory Listing
Modified Mon Mar 12 12:03:12 2012 UTC (3 years, 11 months ago) by gpertea
fixed bam2fastx bugs

Revision 202 - Directory Listing
Modified Mon Mar 12 03:59:38 2012 UTC (3 years, 11 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 (3 years, 11 months ago) by gpertea

Revision 200 - Directory Listing
Modified Fri Mar 9 22:25:25 2012 UTC (3 years, 11 months ago) by gpertea

Revision 199 - Directory Listing
Modified Mon Mar 5 17:16:24 2012 UTC (3 years, 11 months ago) by gpertea

Revision 198 - Directory Listing
Modified Sun Feb 26 18:03:46 2012 UTC (3 years, 11 months ago) by gpertea

Revision 197 - Directory Listing
Modified Sun Feb 26 18:02:05 2012 UTC (3 years, 11 months ago) by gpertea
trans.gff3 seems to work

Revision 196 - Directory Listing
Modified Fri Feb 24 22:48:54 2012 UTC (3 years, 11 months ago) by gpertea
wip gffread trans-splice

Revision 195 - Directory Listing
Modified Thu Feb 23 22:37:36 2012 UTC (3 years, 11 months ago) by gpertea
gff wip

Revision 194 - Directory Listing
Modified Tue Feb 21 21:19:11 2012 UTC (3 years, 11 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 (3 years, 11 months ago) by gpertea

Revision 192 - Directory Listing
Modified Fri Feb 17 23:43:57 2012 UTC (3 years, 11 months ago) by gpertea

Revision 191 - Directory Listing
Modified Fri Feb 17 23:33:25 2012 UTC (3 years, 11 months ago) by gpertea

Revision 190 - Directory Listing
Modified Fri Feb 17 23:33:17 2012 UTC (3 years, 11 months ago) by gpertea

Revision 189 - Directory Listing
Modified Fri Feb 17 23:08:53 2012 UTC (3 years, 11 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 (3 years, 11 months ago) by gpertea
fqtrim works

Revision 187 - Directory Listing
Modified Fri Feb 17 05:42:21 2012 UTC (3 years, 11 months ago) by gpertea
fqtrim

Revision 186 - Directory Listing
Modified Thu Feb 16 22:15:58 2012 UTC (3 years, 11 months ago) by gpertea
adjust safelen threshold from 12 to 16

Revision 185 - Directory Listing
Modified Thu Feb 16 22:05:42 2012 UTC (3 years, 11 months ago) by gpertea

Revision 184 - Directory Listing
Modified Thu Feb 16 21:59:44 2012 UTC (3 years, 11 months ago) by gpertea
works

Revision 183 - Directory Listing
Modified Thu Feb 16 21:59:33 2012 UTC (3 years, 11 months ago) by gpertea
works

Revision 182 - Directory Listing
Modified Thu Feb 16 21:33:27 2012 UTC (3 years, 11 months ago) by gpertea

Revision 181 - Directory Listing
Modified Thu Feb 16 21:24:29 2012 UTC (3 years, 11 months ago) by gpertea
fqtrim works

Revision 180 - Directory Listing
Modified Thu Feb 16 21:24:04 2012 UTC (3 years, 11 months ago) by gpertea
works probably

Revision 179 - Directory Listing
Modified Thu Feb 16 16:23:45 2012 UTC (3 years, 11 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 (3 years, 11 months ago) by gpertea
fqtrim

Revision 177 - Directory Listing
Modified Thu Feb 16 07:10:32 2012 UTC (3 years, 11 months ago) by gpertea
collectSeeds unified

Revision 176 - Directory Listing
Modified Thu Feb 16 03:47:16 2012 UTC (3 years, 11 months ago) by gpertea
fqtrim reworked

Revision 175 - Directory Listing
Modified Thu Feb 16 03:46:59 2012 UTC (3 years, 11 months ago) by gpertea

Revision 174 - Directory Listing
Modified Wed Feb 15 21:04:38 2012 UTC (3 years, 11 months ago) by gpertea
wip fqtrim

Revision 173 - Directory Listing
Modified Wed Feb 15 03:34:29 2012 UTC (3 years, 11 months ago) by gpertea
wip fqtrim

Revision 172 - Directory Listing
Modified Wed Feb 15 03:33:40 2012 UTC (3 years, 11 months ago) by gpertea
wip fqtrim

Revision 171 - Directory Listing
Modified Tue Feb 14 22:36:26 2012 UTC (3 years, 11 months ago) by gpertea
wip fqtrim

Revision 170 - Directory Listing
Modified Tue Feb 14 22:35:51 2012 UTC (3 years, 11 months ago) by gpertea
wip fqtrim

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

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

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

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

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

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

Revision 162 - Directory Listing
Modified Tue Feb 7 19:27:55 2012 UTC (4 years ago) by gpertea
initial map_report commit

Revision 161 - Directory Listing
Modified Tue Feb 7 19:27:04 2012 UTC (4 years ago) by gpertea
adding map_report (raw counts cuffdiff)

Revision 160 - Directory Listing
Modified Fri Feb 3 15:31:57 2012 UTC (4 years ago) by gpertea
added fq_extract script

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

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

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

Revision 156 - Directory Listing
Modified Fri Jan 27 18:29:55 2012 UTC (4 years ago) by gpertea
adding refactored TinyThread++ code

Revision 155 - Directory Listing
Modified Wed Jan 25 21:06:46 2012 UTC (4 years ago) by gpertea
fix for a subtle XLocus building bug

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

Revision 153 - Directory Listing
Modified Fri Jan 20 22:35:32 2012 UTC (4 years ago) by gpertea
still working on trans-splicing/fusions in gff

Revision 152 - Directory Listing
Modified Fri Jan 13 23:08:23 2012 UTC (4 years, 1 month ago) by gpertea
wip

Revision 151 - Directory Listing
Modified Fri Jan 13 22:56:48 2012 UTC (4 years, 1 month ago) by gpertea
wip: trans-spliced and fusion transcripts

Revision 150 - Directory Listing
Modified Fri Jan 13 17:20:39 2012 UTC (4 years, 1 month 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 (4 years, 1 month ago) by gpertea
fixed crash when given input file is '-'

Revision 148 - Directory Listing
Modified Thu Dec 22 21:02:45 2011 UTC (4 years, 1 month ago) by gpertea
added mblasm sources

Revision 147 - Directory Listing
Modified Thu Dec 22 21:01:52 2011 UTC (4 years, 1 month ago) by gpertea
adding my old mgblast assembler

Revision 146 - Directory Listing
Modified Thu Dec 22 20:41:43 2011 UTC (4 years, 1 month ago) by gpertea
removed useless operator>

Revision 145 - Directory Listing
Modified Thu Dec 22 19:19:10 2011 UTC (4 years, 1 month ago) by gpertea

Revision 144 - Directory Listing
Modified Thu Dec 22 19:15:46 2011 UTC (4 years, 1 month 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 (4 years, 1 month ago) by gpertea
removed useless operator>

Revision 142 - Directory Listing
Modified Thu Dec 22 19:11:36 2011 UTC (4 years, 1 month ago) by gpertea
removed useless operator>

Revision 141 - Directory Listing
Modified Thu Dec 22 19:11:20 2011 UTC (4 years, 1 month ago) by gpertea

Revision 140 - Directory Listing
Modified Thu Dec 15 22:40:48 2011 UTC (4 years, 1 month ago) by gpertea

Revision 139 - Directory Listing
Modified Thu Dec 15 22:36:13 2011 UTC (4 years, 1 month ago) by gpertea
spliceCigar() implemented, needs testing

Revision 138 - Directory Listing
Modified Wed Dec 14 22:58:39 2011 UTC (4 years, 2 months ago) by gpertea

Revision 137 - Directory Listing
Modified Wed Dec 14 22:58:22 2011 UTC (4 years, 2 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 (4 years, 2 months ago) by gpertea
added my mobile fput/fget scripts

Revision 135 - Directory Listing
Modified Mon Dec 12 22:28:38 2011 UTC (4 years, 2 months ago) by gpertea
wip - SplicedSAMHitFactory() still not implemented

Revision 134 - Directory Listing
Modified Fri Dec 9 17:52:20 2011 UTC (4 years, 2 months ago) by gpertea

Revision 133 - Directory Listing
Modified Fri Dec 9 15:59:14 2011 UTC (4 years, 2 months ago) by gpertea
TODO: detect sam/bam input for samopen

Revision 132 - Directory Listing
Modified Thu Dec 8 02:53:32 2011 UTC (4 years, 2 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 (4 years, 2 months ago) by gpertea
working

Revision 130 - Directory Listing
Modified Thu Dec 8 01:18:08 2011 UTC (4 years, 2 months ago) by gpertea
fixed exon positions

Revision 129 - Directory Listing
Modified Wed Dec 7 20:59:43 2011 UTC (4 years, 2 months ago) by gpertea

Revision 128 - Directory Listing
Modified Wed Dec 7 20:47:58 2011 UTC (4 years, 2 months ago) by gpertea
wip

Revision 127 - Directory Listing
Modified Wed Dec 7 18:31:56 2011 UTC (4 years, 2 months ago) by gpertea

Revision 126 - Directory Listing
Modified Tue Dec 6 22:45:06 2011 UTC (4 years, 2 months ago) by gpertea
wip


Revision 125 - Directory Listing
Modified Tue Dec 6 19:22:50 2011 UTC (4 years, 2 months ago) by gpertea
minor stats formatting

Revision 124 - Directory Listing
Modified Tue Dec 6 04:54:35 2011 UTC (4 years, 2 months ago) by gpertea
GBam wip

Revision 123 - Directory Listing
Modified Mon Dec 5 22:21:21 2011 UTC (4 years, 2 months ago) by gpertea
bamread files

Revision 122 - Directory Listing
Modified Mon Dec 5 22:19:59 2011 UTC (4 years, 2 months ago) by gpertea
bamread project for testing GBam classes

Revision 121 - Directory Listing
Modified Mon Dec 5 22:18:48 2011 UTC (4 years, 2 months ago) by gpertea
added GBam BAM reader/writer classes (wip)

Revision 120 - Directory Listing
Modified Sun Dec 4 01:46:51 2011 UTC (4 years, 2 months ago) by gpertea

Revision 119 - Directory Listing
Modified Sun Dec 4 01:46:18 2011 UTC (4 years, 2 months ago) by gpertea
fixed calculation of Sn for locus

Revision 118 - Directory Listing
Modified Sun Nov 27 21:14:57 2011 UTC (4 years, 2 months ago) by gpertea
fix locus Sn calculation

Revision 117 - Directory Listing
Modified Wed Nov 23 21:27:59 2011 UTC (4 years, 2 months ago) by gpertea
gbs2gff fixes

Revision 116 - Directory Listing
Modified Mon Nov 7 21:25:56 2011 UTC (4 years, 3 months ago) by gpertea
Ensembl conversion corrections

Revision 115 - Directory Listing
Modified Mon Nov 7 21:25:03 2011 UTC (4 years, 3 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 (4 years, 3 months ago) by gpertea
backup scripts updated

Revision 113 - Directory Listing
Modified Mon Nov 7 13:24:06 2011 UTC (4 years, 3 months ago) by gpertea
gb2gff tweaks

Revision 112 - Directory Listing
Modified Tue Nov 1 20:57:08 2011 UTC (4 years, 3 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 (4 years, 3 months ago) by gpertea
wip

Revision 110 - Directory Listing
Modified Wed Oct 12 17:17:00 2011 UTC (4 years, 4 months ago) by gpertea
minor script updates

Revision 109 - Directory Listing
Modified Tue Oct 11 19:50:14 2011 UTC (4 years, 4 months ago) by gpertea
added GStr::reverse(), GAlnExtend stringency tweaks

Revision 108 - Directory Listing
Modified Tue Oct 11 19:49:29 2011 UTC (4 years, 4 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 (4 years, 4 months ago) by gpertea
wip GYarn (threads)

Revision 106 - Directory Listing
Modified Mon Oct 10 21:45:05 2011 UTC (4 years, 4 months ago) by gpertea

Revision 105 - Directory Listing
Modified Mon Oct 10 21:44:55 2011 UTC (4 years, 4 months ago) by gpertea
wip - works?

Revision 104 - Directory Listing
Modified Mon Oct 10 19:34:20 2011 UTC (4 years, 4 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 (4 years, 4 months ago) by gpertea
wip

Revision 102 - Directory Listing
Modified Fri Oct 7 21:44:59 2011 UTC (4 years, 4 months ago) by gpertea
wip

Revision 101 - Directory Listing
Modified Fri Oct 7 21:13:55 2011 UTC (4 years, 4 months ago) by gpertea
adjusting params

Revision 100 - Directory Listing
Modified Fri Oct 7 21:13:33 2011 UTC (4 years, 4 months ago) by gpertea
adjusting params

Revision 99 - Directory Listing
Modified Thu Oct 6 20:49:17 2011 UTC (4 years, 4 months ago) by gpertea
wip

Revision 98 - Directory Listing
Modified Thu Oct 6 20:49:00 2011 UTC (4 years, 4 months ago) by gpertea
wip

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

Revision 96 - Directory Listing
Modified Wed Oct 5 18:31:48 2011 UTC (4 years, 4 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 (4 years, 4 months ago) by gpertea

Revision 94 - Directory Listing
Modified Tue Oct 4 21:27:35 2011 UTC (4 years, 4 months ago) by gpertea
wip

Revision 93 - Directory Listing
Modified Tue Oct 4 12:27:31 2011 UTC (4 years, 4 months ago) by gpertea
added gapped alignment extension code

Revision 92 - Directory Listing
Modified Mon Oct 3 21:36:42 2011 UTC (4 years, 4 months ago) by gpertea
switching to gclib/GAlnExtend

Revision 91 - Directory Listing
Modified Mon Oct 3 20:51:09 2011 UTC (4 years, 4 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 (4 years, 4 months ago) by gpertea
reverseChars() minor edit

Revision 89 - Directory Listing
Modified Mon Oct 3 18:42:24 2011 UTC (4 years, 4 months ago) by gpertea
separate wrappers for 5' and  3' alignments

Revision 88 - Directory Listing
Modified Mon Oct 3 16:34:03 2011 UTC (4 years, 4 months ago) by gpertea
starting to add polyA/T trimming

Revision 87 - Directory Listing
Modified Sun Oct 2 19:12:03 2011 UTC (4 years, 4 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 (4 years, 4 months ago) by gpertea
fixed a few more subtle bugs

Revision 85 - Directory Listing
Modified Fri Sep 30 20:38:13 2011 UTC (4 years, 4 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 (4 years, 4 months ago) by gpertea
wip bad

Revision 83 - Directory Listing
Modified Thu Sep 29 21:32:42 2011 UTC (4 years, 4 months ago) by gpertea
wip

Revision 82 - Directory Listing
Modified Thu Sep 29 20:46:39 2011 UTC (4 years, 4 months ago) by gpertea
wip

Revision 81 - Directory Listing
Modified Thu Sep 29 19:02:24 2011 UTC (4 years, 4 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 (4 years, 4 months ago) by gpertea
wip

Revision 79 - Directory Listing
Modified Wed Sep 28 19:54:42 2011 UTC (4 years, 4 months ago) by gpertea
wip, fixed memory leaks

Revision 78 - Directory Listing
Modified Wed Sep 28 03:20:10 2011 UTC (4 years, 4 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 (4 years, 4 months ago) by gpertea
wip - cutting seeds, finalize()

Revision 76 - Directory Listing
Modified Tue Sep 27 12:37:02 2011 UTC (4 years, 4 months ago) by gpertea
u

Revision 75 - Directory Listing
Modified Tue Sep 27 02:24:57 2011 UTC (4 years, 4 months ago) by gpertea
implementing GreedyAlign for best rseeds etc.

Revision 74 - Directory Listing
Modified Tue Sep 27 01:22:37 2011 UTC (4 years, 4 months ago) by gpertea
added seqalign files

Revision 73 - Directory Listing
Modified Tue Sep 27 01:20:53 2011 UTC (4 years, 4 months ago) by gpertea
creating seqalign storage

Revision 72 - Directory Listing
Modified Tue Sep 27 01:20:21 2011 UTC (4 years, 4 months ago) by gpertea
reversed gene_id requirement for TSS clustering

Revision 71 - Directory Listing
Modified Fri Sep 23 19:23:49 2011 UTC (4 years, 4 months ago) by gpertea
gridx fixed to export PERL5LIB and PYTHONPATH

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

Revision 69 - Directory Listing
Modified Mon Sep 19 21:00:41 2011 UTC (4 years, 4 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, 4 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, 4 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 (4 years, 4 months ago) by gpertea
made some Flybase GFF3 "errors" non-fatal

Revision 65 - Directory Listing
Modified Fri Sep 16 18:33:19 2011 UTC (4 years, 4 months ago) by gpertea

Revision 64 - Directory Listing
Modified Fri Sep 9 20:58:16 2011 UTC (4 years, 5 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 (4 years, 5 months ago) by gpertea

Revision 62 - Directory Listing
Modified Fri Sep 9 20:19:10 2011 UTC (4 years, 5 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 (4 years, 5 months ago) by gpertea
removed startChanged flag, not needed

Revision 60 - Directory Listing
Modified Fri Sep 9 18:00:55 2011 UTC (4 years, 5 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 (4 years, 5 months ago) by gpertea
finally fixed the placeGf clustering bug

Revision 58 - Directory Listing
Modified Fri Sep 9 14:01:30 2011 UTC (4 years, 5 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 (4 years, 5 months ago) by gpertea
wip

Revision 56 - Directory Listing
Modified Thu Sep 8 05:47:09 2011 UTC (4 years, 5 months ago) by gpertea
RPS20P29, ENSG00000241828 not collapsing

Revision 55 - Directory Listing
Modified Thu Sep 8 05:46:53 2011 UTC (4 years, 5 months ago) by gpertea
RPS20P29, ENSG00000241828 not collapsing

Revision 54 - Directory Listing
Modified Thu Sep 8 05:46:16 2011 UTC (4 years, 5 months ago) by gpertea
debug RPS20P29 ENSG00000241828 not collapsing

Revision 53 - Directory Listing
Modified Thu Sep 8 02:43:56 2011 UTC (4 years, 5 months ago) by gpertea

Revision 52 - Directory Listing
Modified Thu Sep 8 02:43:30 2011 UTC (4 years, 5 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 (4 years, 5 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 (4 years, 5 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 (4 years, 5 months ago) by gpertea
minor edits

Revision 48 - Directory Listing
Modified Wed Sep 7 16:07:32 2011 UTC (4 years, 5 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 (4 years, 5 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 (4 years, 5 months ago) by gpertea
fixed GStr[-2] bug

Revision 45 - Directory Listing
Modified Tue Sep 6 18:19:20 2011 UTC (4 years, 5 months ago) by gpertea
added gfview files

Revision 44 - Directory Listing
Modified Tue Sep 6 18:15:55 2011 UTC (4 years, 5 months ago) by gpertea
added gfview

Revision 43 - Directory Listing
Modified Tue Sep 6 17:41:50 2011 UTC (4 years, 5 months ago) by gpertea
m

Revision 42 - Directory Listing
Modified Tue Sep 6 17:40:45 2011 UTC (4 years, 5 months ago) by gpertea
minor edit

Revision 41 - Directory Listing
Modified Sat Aug 27 16:58:00 2011 UTC (4 years, 5 months ago) by gpertea
added fix for fileExists() under MSVC

Revision 40 - Directory Listing
Modified Sat Aug 27 16:48:50 2011 UTC (4 years, 5 months ago) by gpertea
added clview files and examples

Revision 39 - Directory Listing
Modified Sat Aug 27 15:50:52 2011 UTC (4 years, 5 months ago) by gpertea
clview added

Revision 38 - Directory Listing
Modified Sat Aug 27 15:42:15 2011 UTC (4 years, 5 months ago) by gpertea

Revision 37 - Directory Listing
Modified Mon Aug 22 16:17:34 2011 UTC (4 years, 5 months ago) by gpertea
wip

Revision 36 - Directory Listing
Modified Mon Aug 22 15:56:21 2011 UTC (4 years, 5 months ago) by gpertea

Revision 35 - Directory Listing
Modified Fri Aug 5 18:47:20 2011 UTC (4 years, 6 months ago) by gpertea
wip

Revision 34 - Directory Listing
Modified Wed Aug 3 22:15:52 2011 UTC (4 years, 6 months ago) by gpertea
wip segment_juncs

Revision 33 - Directory Listing
Modified Wed Aug 3 17:02:56 2011 UTC (4 years, 6 months ago) by gpertea
wip conversion to SAM processing

Revision 32 - Directory Listing
Modified Tue Aug 2 22:04:47 2011 UTC (4 years, 6 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, 6 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, 6 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, 6 months ago) by gpertea
adding tophat source work

Revision 28 - Directory Listing
Modified Tue Aug 2 21:23:26 2011 UTC (4 years, 6 months ago) by gpertea
adding tophat_cpp dir

Revision 27 - Directory Listing
Modified Wed Jul 27 20:43:37 2011 UTC (4 years, 6 months ago) by gpertea

Revision 26 - Directory Listing
Modified Wed Jul 27 19:39:27 2011 UTC (4 years, 6 months ago) by gpertea
added missing gff_utils source

Revision 25 - Directory Listing
Modified Tue Jul 26 21:50:53 2011 UTC (4 years, 6 months ago) by gpertea

Revision 24 - Directory Listing
Modified Tue Jul 26 21:46:39 2011 UTC (4 years, 6 months ago) by gpertea

Revision 23 - Directory Listing
Modified Tue Jul 26 21:44:38 2011 UTC (4 years, 6 months ago) by gpertea
adding misc scripts

Revision 22 - Directory Listing
Modified Tue Jul 26 21:43:45 2011 UTC (4 years, 6 months ago) by gpertea
various scripts

Revision 21 - Directory Listing
Modified Mon Jul 18 22:35:05 2011 UTC (4 years, 6 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 (4 years, 6 months ago) by gpertea
added cuffcompare sources

Revision 19 - Directory Listing
Modified Mon Jul 18 21:07:43 2011 UTC (4 years, 6 months ago) by gpertea
mkdir cuffcompare

Revision 18 - Directory Listing
Modified Mon Jul 18 21:00:21 2011 UTC (4 years, 6 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 (4 years, 6 months ago) by gpertea
sync with local source

Revision 16 - Directory Listing
Modified Mon Jul 18 20:56:02 2011 UTC (4 years, 6 months ago) by gpertea
sync with local source

Revision 15 - Directory Listing
Modified Mon Jul 18 20:53:45 2011 UTC (4 years, 6 months ago) by gpertea
sync with local src

Revision 14 - Directory Listing
Modified Mon Jul 18 20:36:48 2011 UTC (4 years, 6 months ago) by gpertea
added old trimpoly code just for archive

Revision 13 - Directory Listing
Modified Mon Jul 18 20:35:43 2011 UTC (4 years, 6 months ago) by gpertea
sync with my local source

Revision 12 - Directory Listing
Modified Wed Jan 26 19:05:05 2011 UTC (5 years ago) by gpertea
added qv-threshold trimming

Revision 11 - Directory Listing
Modified Tue Mar 23 18:03:12 2010 UTC (5 years, 10 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 (5 years, 10 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 (5 years, 10 months ago) by gpertea
fixed bug causing overtrimming

Revision 8 - Directory Listing
Modified Mon Mar 22 22:11:25 2010 UTC (5 years, 10 months ago) by gpertea
added cdbfasta source files

Revision 7 - Directory Listing
Modified Mon Mar 22 22:08:51 2010 UTC (5 years, 10 months ago) by gpertea
mkdir cdbfasta

Revision 6 - Directory Listing
Modified Mon Mar 22 22:07:27 2010 UTC (5 years, 10 months ago) by gpertea
added gffread sources

Revision 5 - Directory Listing
Modified Mon Mar 22 22:06:27 2010 UTC (5 years, 10 months ago) by gpertea
mkdir gffread

Revision 4 - Directory Listing
Modified Mon Mar 22 22:05:23 2010 UTC (5 years, 10 months ago) by gpertea
initial commit

Revision 3 - Directory Listing
Modified Mon Mar 22 22:04:34 2010 UTC (5 years, 10 months ago) by gpertea
mkdir

Revision 2 - Directory Listing
Modified Mon Mar 22 22:03:27 2010 UTC (5 years, 10 months ago) by gpertea
added my gclib source files

Revision 1 - Directory Listing
Added Mon Mar 22 22:01:50 2010 UTC (5 years, 10 months ago) by gpertea
import