ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/gclib/gclib
Sticky Revision:
Sort logs by:
Revision 310 - Directory Listing
Modified Fri Mar 22 20:06:27 2013 UTC (3 years, 1 month ago) by gpertea
sync with igm repo

Revision 301 - Directory Listing
Modified Fri Oct 26 12:44:32 2012 UTC (3 years, 6 months ago) by gpertea
minor refactoring


Revision 299 - Directory Listing
Modified Wed Oct 24 22:40:33 2012 UTC (3 years, 6 months ago) by gpertea
wip

Revision 295 - Directory Listing
Modified Mon Oct 22 19:01:32 2012 UTC (3 years, 6 months ago) by gpertea
minor GVec change to Add() function

Revision 287 - Directory Listing
Modified Mon Oct 15 18:37:20 2012 UTC (3 years, 6 months ago) by gpertea

Revision 286 - Directory Listing
Modified Mon Oct 15 17:31:47 2012 UTC (3 years, 6 months ago) by gpertea
slight mods for rejoin use

Revision 268 - Directory Listing
Modified Thu Oct 4 14:04:46 2012 UTC (3 years, 6 months ago) by gpertea

Revision 264 - Directory Listing
Modified Mon Aug 27 18:21:11 2012 UTC (3 years, 8 months ago) by gpertea
minor refactoring etc

Revision 258 - Directory Listing
Modified Tue Jun 26 22:29:50 2012 UTC (3 years, 10 months ago) by gpertea
commented out saprintf(), not used

Revision 255 - Directory Listing
Modified Mon Jun 4 20:02:45 2012 UTC (3 years, 10 months ago) by gpertea
minor reformatting by Cole

Revision 253 - Directory Listing
Modified Tue May 29 15:21:30 2012 UTC (3 years, 11 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, 11 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, 11 months ago) by gpertea

Revision 250 - Directory Listing
Modified Thu May 24 18:21:10 2012 UTC (3 years, 11 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, 11 months ago) by gpertea
moved sorting into GVec.hh

Revision 248 - Directory Listing
Modified Wed May 23 22:10:55 2012 UTC (3 years, 11 months ago) by gpertea
put GVec and GPVec in GVec.hh, added GIntervalTree.hh

Revision 235 - Directory Listing
Modified Mon Apr 23 21:31:55 2012 UTC (4 years ago) by gpertea
some clarifications in CIGAR operation parsing

Revision 234 - Directory Listing
Modified Wed Apr 11 21:05:36 2012 UTC (4 years ago) by gpertea
fixed find_tag() to use the bam_aux_get()

Revision 232 - Directory Listing
Modified Wed Apr 4 18:36:58 2012 UTC (4 years ago) by gpertea
Daehwan fixed an egregious bug in find_tag()

Revision 227 - Directory Listing
Modified Mon Mar 26 21:28:07 2012 UTC (4 years, 1 month ago) by gpertea

Revision 225 - Directory Listing
Modified Mon Mar 26 12:07:13 2012 UTC (4 years, 1 month ago) by gpertea

Revision 214 - Directory Listing
Modified Wed Mar 14 01:47:41 2012 UTC (4 years, 1 month ago) by gpertea
fixed ugly bug in GBamRecord::find_tag()

Revision 198 - Directory Listing
Modified Sun Feb 26 18:03:46 2012 UTC (4 years, 2 months ago) by gpertea

Revision 197 - Directory Listing
Modified Sun Feb 26 18:02:05 2012 UTC (4 years, 2 months ago) by gpertea
trans.gff3 seems to work

Revision 196 - Directory Listing
Modified Fri Feb 24 22:48:54 2012 UTC (4 years, 2 months ago) by gpertea
wip gffread trans-splice

Revision 195 - Directory Listing
Modified Thu Feb 23 22:37:36 2012 UTC (4 years, 2 months ago) by gpertea
gff wip

Revision 194 - Directory Listing
Modified Tue Feb 21 21:19:11 2012 UTC (4 years, 2 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 (4 years, 2 months ago) by gpertea

Revision 191 - Directory Listing
Modified Fri Feb 17 23:33:25 2012 UTC (4 years, 2 months ago) by gpertea

Revision 188 - Directory Listing
Modified Fri Feb 17 05:42:37 2012 UTC (4 years, 2 months ago) by gpertea
fqtrim works

Revision 186 - Directory Listing
Modified Thu Feb 16 22:15:58 2012 UTC (4 years, 2 months ago) by gpertea
adjust safelen threshold from 12 to 16

Revision 184 - Directory Listing
Modified Thu Feb 16 21:59:44 2012 UTC (4 years, 2 months ago) by gpertea
works

Revision 181 - Directory Listing
Modified Thu Feb 16 21:24:29 2012 UTC (4 years, 2 months ago) by gpertea
fqtrim works

Revision 179 - Directory Listing
Modified Thu Feb 16 16:23:45 2012 UTC (4 years, 2 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 (4 years, 2 months ago) by gpertea
fqtrim

Revision 176 - Directory Listing
Modified Thu Feb 16 03:47:16 2012 UTC (4 years, 2 months ago) by gpertea
fqtrim reworked

Revision 174 - Directory Listing
Modified Wed Feb 15 21:04:38 2012 UTC (4 years, 2 months ago) by gpertea
wip fqtrim

Revision 173 - Directory Listing
Modified Wed Feb 15 03:34:29 2012 UTC (4 years, 2 months ago) by gpertea
wip fqtrim

Revision 171 - Directory Listing
Modified Tue Feb 14 22:36:26 2012 UTC (4 years, 2 months ago) by gpertea
wip fqtrim

Revision 156 - Directory Listing
Modified Fri Jan 27 18:29:55 2012 UTC (4 years, 3 months ago) by gpertea
adding refactored TinyThread++ code

Revision 153 - Directory Listing
Modified Fri Jan 20 22:35:32 2012 UTC (4 years, 3 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 (4 years, 3 months ago) by gpertea
wip

Revision 151 - Directory Listing
Modified Fri Jan 13 22:56:48 2012 UTC (4 years, 3 months ago) by gpertea
wip: trans-spliced and fusion transcripts

Revision 150 - Directory Listing
Modified Fri Jan 13 17:20:39 2012 UTC (4 years, 3 months ago) by gpertea
fixed parsing bug for extractAttr(); 
Gstrcmp() and Gstricmp() take a 3rd optional param to make them work like strncmp()

Revision 144 - Directory Listing
Modified Thu Dec 22 19:15:46 2011 UTC (4 years, 4 months ago) by gpertea
added GBitVec.h; removed operator> requirement for sorted vectors; swap() is now template Gswap()

Revision 133 - Directory Listing
Modified Fri Dec 9 15:59:14 2011 UTC (4 years, 4 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, 4 months ago) by gpertea
GBam working; fixed serious memory leak in GVec::setCapacity()

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

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

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

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


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

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

Revision 115 - Directory Listing
Modified Mon Nov 7 21:25:03 2011 UTC (4 years, 5 months ago) by gpertea
fixed horrendous bug in GList.hh (resizing GVec)

Revision 109 - Directory Listing
Modified Tue Oct 11 19:50:14 2011 UTC (4 years, 6 months ago) by gpertea
added GStr::reverse(), GAlnExtend stringency tweaks

Revision 107 - Directory Listing
Modified Tue Oct 11 12:31:50 2011 UTC (4 years, 6 months ago) by gpertea
wip GYarn (threads)

Revision 106 - Directory Listing
Modified Mon Oct 10 21:45:05 2011 UTC (4 years, 6 months ago) by gpertea

Revision 104 - Directory Listing
Modified Mon Oct 10 19:34:20 2011 UTC (4 years, 6 months ago) by gpertea
fixed GVec, GArray to use new[] instead of malloc

Revision 101 - Directory Listing
Modified Fri Oct 7 21:13:55 2011 UTC (4 years, 6 months ago) by gpertea
adjusting params

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

Revision 96 - Directory Listing
Modified Wed Oct 5 18:31:48 2011 UTC (4 years, 6 months ago) by gpertea
moved match_LeftEnd() and match_RightEnd() to GAlnExtend

Revision 93 - Directory Listing
Modified Tue Oct 4 12:27:31 2011 UTC (4 years, 6 months ago) by gpertea
added gapped alignment extension code

Revision 90 - Directory Listing
Modified Mon Oct 3 18:45:22 2011 UTC (4 years, 6 months ago) by gpertea
reverseChars() minor edit

Revision 66 - Directory Listing
Modified Fri Sep 16 18:33:54 2011 UTC (4 years, 7 months ago) by gpertea
made some Flybase GFF3 "errors" non-fatal

Revision 63 - Directory Listing
Modified Fri Sep 9 20:19:21 2011 UTC (4 years, 7 months ago) by gpertea

Revision 60 - Directory Listing
Modified Fri Sep 9 18:00:55 2011 UTC (4 years, 7 months ago) by gpertea
made sure Swap (Exchange) is available for GList, GVec

Revision 55 - Directory Listing
Modified Thu Sep 8 05:46:53 2011 UTC (4 years, 7 months ago) by gpertea
RPS20P29, ENSG00000241828 not collapsing

Revision 51 - Directory Listing
Modified Thu Sep 8 01:02:11 2011 UTC (4 years, 7 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, 7 months ago) by gpertea
fixed a loading bug when a CDS was given to a monoFeature() with a self-exon

Revision 41 - Directory Listing
Modified Sat Aug 27 16:58:00 2011 UTC (4 years, 8 months ago) by gpertea
added fix for fileExists() under MSVC

Revision 36 - Directory Listing
Modified Mon Aug 22 15:56:21 2011 UTC (4 years, 8 months ago) by gpertea

Revision 18 - Directory Listing
Modified Mon Jul 18 21:00:21 2011 UTC (4 years, 9 months ago) by gpertea
added a few more source files, test code

Revision 16 - Directory Listing
Modified Mon Jul 18 20:56:02 2011 UTC (4 years, 9 months ago) by gpertea
sync with local source

Revision 2 - Directory Listing
Modified Mon Mar 22 22:03:27 2010 UTC (6 years, 1 month ago) by gpertea
added my gclib source files

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