/[v1]/trunk/c++/src/algo/align/ngalign/merge_aligner.cpp
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Log of /trunk/c++/src/algo/align/ngalign/merge_aligner.cpp

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Revision 95346 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Nov 8 14:35:53 2021 UTC (2 years, 5 months ago) by mozese2
File length: 8570 byte(s)
Diff to previous 72271 
With the new optimizations, CTreeAlignMerger should be created once and used repeatedly within one thread, not created within a tight loop
JIRA GP-31879
Revision 72271 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 27 16:55:47 2016 UTC (8 years ago) by boukn
File length: 8648 byte(s)
Diff to previous 71429 
Commit for allowdupes cleanup, from static to member
Revision 71429 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Mar 3 20:39:42 2016 UTC (8 years, 2 months ago) by whlavina
File length: 8542 byte(s)
Diff to previous 64926 
Reduce logging in gbalign_wnode.
JIRA: GP-16503.
Revision 64926 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Oct 23 16:04:54 2014 UTC (9 years, 6 months ago) by boukn
File length: 8558 byte(s)
Diff to previous 64516 
JIRA:GP-10180: Most errors have changed from 'continue on if possible' to 'throw to the caller'
Revision 64516 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Sep 19 02:49:56 2014 UTC (9 years, 7 months ago) by whlavina
File length: 8581 byte(s)
Diff to previous 64478 
Flip mixed up old vs new tree align merger.
JIRA: GP-9754.
Revision 64478 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 17 03:22:34 2014 UTC (9 years, 7 months ago) by whlavina
File length: 8581 byte(s)
Diff to previous 63076 
Expose option for choosing among align merge algorithms.
JIRA: GP-9754.
Revision 63076 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue May 27 16:23:17 2014 UTC (9 years, 11 months ago) by dicuccio
File length: 8358 byte(s)
Diff to previous 63010 
Back to CAlignCleanup
JIRA: GP-8216
Revision 63010 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu May 22 15:07:57 2014 UTC (9 years, 11 months ago) by dicuccio
File length: 8358 byte(s)
Diff to previous 63001 
...and back to tree align merge
JIRA: GP-8454
Revision 63001 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu May 22 01:15:57 2014 UTC (9 years, 11 months ago) by dicuccio
File length: 8358 byte(s)
Diff to previous 62756 
Revert use of CTreeAlignMerger
JIRA: GP-8454
Revision 62756 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon May 5 19:08:20 2014 UTC (10 years ago) by dicuccio
File length: 8358 byte(s)
Diff to previous 62669 
Re-enable tree merge algorithm
JIRA: GP-8216, GP-8267
Revision 62669 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Apr 28 01:41:18 2014 UTC (10 years ago) by dicuccio
File length: 8358 byte(s)
Diff to previous 62666 
Back to CAlignCleanup again
JIRA: GP-8216
Revision 62666 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Apr 26 18:49:30 2014 UTC (10 years ago) by dicuccio
File length: 8358 byte(s)
Diff to previous 62665 
Re-enable merge tree; looks like Nathan's fix for more fields in dtor fixes the out-of-memory issues
JIRA: GP-8216
Revision 62665 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Apr 26 18:21:56 2014 UTC (10 years ago) by dicuccio
File length: 8358 byte(s)
Diff to previous 62619 
Revert to CAlignCleanup
JIRA: GP-8216
Revision 62619 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Apr 24 14:30:01 2014 UTC (10 years ago) by dicuccio
File length: 8358 byte(s)
Diff to previous 51502 
Enable mergetree build
Switch to mergetree algorithm in NG aligner
JIRA: CXX-4610, GP-7162
Revision 51502 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Oct 7 14:49:06 2011 UTC (12 years, 7 months ago) by boukn
File length: 8259 byte(s)
Diff to previous 47983 
JIRA CG-873: Added an option to genomic_compart to sort
  by alignment score instead of alignment length.
  NG's Merge plugin will use both methods
Revision 47983 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Nov 21 15:23:40 2010 UTC (13 years, 5 months ago) by dicuccio
File length: 7836 byte(s)
Diff to previous 47303 
Use genomic compartmentalizer when merging
JIRA: GP-1202
Revision 47303 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 27 13:41:20 2010 UTC (13 years, 7 months ago) by dicuccio
File length: 7042 byte(s)
Diff to previous 47239 
Retabify.  Remove executable bit.
Revision 47239 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 22 19:26:50 2010 UTC (13 years, 7 months ago) by boukn
File length: 7032 byte(s)
Diff to previous 44496 
Modified CQuerySet to accept a gencoll assembly, 
  and store alignments per-assembly, per-subject.
  Filtering now happens on a per-query, per-assembly level.
Revision 44496 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 19 16:44:34 2010 UTC (14 years, 3 months ago) by boukn
File length: 6872 byte(s)
Diff to previous 44467 
Added report feature for which plugin every alignment was created by
Revision 44467 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jan 15 17:32:41 2010 UTC (14 years, 3 months ago) by dicuccio
File length: 6881 byte(s)
Diff to previous 44373 
Drop unneeded executable bit
Revision 44373 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jan 8 19:20:15 2010 UTC (14 years, 4 months ago) by boukn
File length: 6881 byte(s)
Diff to previous 44325 
  Sorting functions will now use > instead of
    >= which caused crashes with std::sort
Revision 44325 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 5 16:23:13 2010 UTC (14 years, 4 months ago) by boukn
File length: 6861 byte(s)
Diff to previous 44281 
Fixed some bugs instance length filtering,
  alignment merging order, and inversion merging
Revision 44281 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Dec 30 18:25:12 2009 UTC (14 years, 4 months ago) by boukn
File length: 5953 byte(s)
Diff to previous 43363 
Before merging, alignments will be split up
 by Query strand, and merged one strand at a time.
Revision 43363 - (view) (download) (as text) (annotate) - [select for diffs]
Added Thu Oct 1 14:38:07 2009 UTC (14 years, 7 months ago) by boukn
File length: 4889 byte(s) 
Added CMergeAligner

CBlastAligner can set the SetSoftFiltering() level
 with BlastDb subject sets.

Modified CInstancedAligner to use a new distance-limited
 instance finder. So duplicate alignments on the same
 subject can now both be found.

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