[v1] Log of /trunk/c++/src/algo/gnomon/annot.cpp

Revision 101964 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 12 17:29:59 2024 UTC (2 months ago) by souvorov
File length: 37982 byte(s)
Diff to previous 101630

Fix int32 overflow JIRA:GP-37530

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Modified Wed Jan 17 15:20:58 2024 UTC (3 months, 4 weeks ago) by souvorov
File length: 37908 byte(s)
Diff to previous 100690

Fix gene models nested in introns JIRA:GP-36935

Revision 100690 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Aug 30 14:46:42 2023 UTC (8 months, 2 weeks ago) by souvorov
File length: 31703 byte(s)
Diff to previous 100465

Compact version of PhyloCSF scores JIRA:GP-30239

Revision 100465 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Aug 3 17:24:45 2023 UTC (9 months, 2 weeks ago) by souvorov
File length: 31991 byte(s)
Diff to previous 100392

Use PhyloCSF scores JIRA:GP-30239

Revision 100392 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 27 15:57:51 2023 UTC (9 months, 3 weeks ago) by souvorov
File length: 32493 byte(s)
Diff to previous 92075

Fix Clang warnings JIRA:GP-36000

Revision 92075 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Dec 21 15:12:57 2020 UTC (3 years, 4 months ago) by grichenk
File length: 32928 byte(s)
Diff to previous 91689

Replaced auto_ptr with unique_ptr. JIRA CXX-11620

Revision 91689 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Nov 30 16:00:57 2020 UTC (3 years, 5 months ago) by souvorov
File length: 32924 byte(s)
Diff to previous 91015

Fix compilation warnings

Revision 91015 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Aug 24 14:24:47 2020 UTC (3 years, 8 months ago) by souvorov
File length: 32954 byte(s)
Diff to previous 82897

Prevent integer overflow in gnomon JIRA: GP-29469

Revision 82897 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 12 18:38:13 2018 UTC (5 years, 10 months ago) by souvorov
File length: 32981 byte(s)
Diff to previous 67192

Remove overlapping partial chains JIRA:GP-24575

Revision 67192 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Apr 27 14:27:13 2015 UTC (9 years ago) by souvorov
File length: 31883 byte(s)
Diff to previous 65693

Use RNA-Seq alignments for model correction JIRA:GP-11166

Revision 65693 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Dec 22 16:08:03 2014 UTC (9 years, 4 months ago) by souvorov
File length: 31850 byte(s)
Diff to previous 63286

Annotate for selenoproteins JIRA:GP-10475

Revision 63286 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 13 14:38:39 2014 UTC (9 years, 11 months ago) by souvorov
File length: 31479 byte(s)
Diff to previous 63269

Make gnomon gap aware JIRA:GP-8578

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Modified Thu Jun 12 17:01:09 2014 UTC (9 years, 11 months ago) by souvorov
File length: 31349 byte(s)
Diff to previous 63073

Fix identification of nested models JIRA:GP-8734

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Modified Tue May 27 14:58:14 2014 UTC (9 years, 11 months ago) by souvorov
File length: 31135 byte(s)
Diff to previous 60182

Create gap-filled models onle with 45nt CDS on the genome JIRA:GP-8519

Revision 60182 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Oct 31 14:19:11 2013 UTC (10 years, 6 months ago) by souvorov
File length: 31095 byte(s)
Diff to previous 60091

Remove UTR-only gap-filled models JIRA:GP-6305

Revision 60091 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Oct 23 19:00:04 2013 UTC (10 years, 6 months ago) by souvorov
File length: 30394 byte(s)
Diff to previous 59950

Prevent random (very rare) loss of partial chains with a start and open 5' end

Revision 59950 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Sep 27 17:52:55 2013 UTC (10 years, 7 months ago) by souvorov
File length: 30163 byte(s)
Diff to previous 59851

Make gnomon annot aware of genomic gap filling JIRA:GP-5360

Revision 59851 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Sep 21 20:26:30 2013 UTC (10 years, 7 months ago) by souvorov
File length: 30060 byte(s)
Diff to previous 57677

Remove sraintrons/srailand functionality which has never been used

Revision 57677 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Apr 4 13:51:41 2013 UTC (11 years, 1 month ago) by souvorov
File length: 31223 byte(s)
Diff to previous 57059

Allow partial nessted genes JIRA:GP-3902

Revision 57059 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Feb 1 15:30:00 2013 UTC (11 years, 3 months ago) by souvorov
File length: 22788 byte(s)
Diff to previous 57016

Remove -tolerance from annot_wnode JIRA:GP-3620

Revision 57016 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jan 28 18:08:46 2013 UTC (11 years, 3 months ago) by souvorov
File length: 23003 byte(s)
Diff to previous 56958

move gene finding from Gnomon to Chainer JIRA:GP-3620

Revision 56958 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 22 20:21:51 2013 UTC (11 years, 3 months ago) by souvorov
File length: 24185 byte(s)
Diff to previous 56904

revisions for Gnomon minlen filter and RNAseq JIRA:GP-3614

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Modified Thu Jan 17 14:04:38 2013 UTC (11 years, 4 months ago) by souvorov
File length: 25224 byte(s)
Diff to previous 56349

Gnomon non-coding RNA spec revisions JIRA:GP-3541

Revision 56349 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Nov 21 15:03:01 2012 UTC (11 years, 5 months ago) by souvorov
File length: 25331 byte(s)
Diff to previous 54495

Remove assert for overlaping genes; correct handling of indels in start/stop

Revision 54495 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu May 17 14:41:54 2012 UTC (12 years ago) by souvorov
File length: 25033 byte(s)
Diff to previous 53297

Give more weight to CDS length and allow connect nested gene the the external gene

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Modified Wed Mar 7 14:15:01 2012 UTC (12 years, 2 months ago) by chetvern
File length: 24758 byte(s)
Diff to previous 51148

Do not run ab initio on short contigs (JIRA: GP-1477)

Revision 51148 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Sep 9 14:41:52 2011 UTC (12 years, 8 months ago) by souvorov
File length: 24672 byte(s)
Diff to previous 48593

Major RNA-Seq overhaul JIRA: GP-1174

Revision 48593 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Feb 7 18:14:37 2011 UTC (13 years, 3 months ago) by chetvern
File length: 24484 byte(s)
Diff to previous 46630

Do not try to trim in triplets. It is not necessarily on codon boundary anyway

Revision 46630 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jul 27 13:54:05 2010 UTC (13 years, 9 months ago) by chetvern
File length: 24627 byte(s)
Diff to previous 46555

Warnings heeded

Revision 46555 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jul 19 19:28:09 2010 UTC (13 years, 10 months ago) by chetvern
File length: 24622 byte(s)
Diff to previous 45282

Truncate leading and trailing Ns off model mRNAs (JIRA: GPI-801)

Revision 45282 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 29 19:07:22 2010 UTC (14 years, 1 month ago) by chetvern
File length: 24366 byte(s)
Diff to previous 44608

Do not bypass model status finalization when -nognomon

Revision 44608 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 26 16:41:22 2010 UTC (14 years, 3 months ago) by chetvern
File length: 24335 byte(s)
Diff to previous 44570

arg.AsInputFile() is not thread safe

Revision 44570 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jan 22 19:48:38 2010 UTC (14 years, 3 months ago) by ucko
File length: 24287 byte(s)
Diff to previous 44569

Use appropriate syntax ("..." rather than <...>) in the #include
directive for the internal gnomon_engine.hpp header.

Revision 44569 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jan 22 18:50:10 2010 UTC (14 years, 3 months ago) by souvorov
File length: 24287 byte(s)
Diff to previous 44235

Short read introns and islands

Revision 44235 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Dec 23 14:52:56 2009 UTC (14 years, 4 months ago) by chetvern
File length: 22703 byte(s)
Diff to previous 44184

Sequence masking.
Moved args.

Revision 44184 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Dec 16 19:03:55 2009 UTC (14 years, 5 months ago) by chetvern
File length: 21621 byte(s)
Diff to previous 44098

Moved RemoveTrailingNs to the library (JIRA: GP-662)

Revision 44098 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Dec 8 18:33:20 2009 UTC (14 years, 5 months ago) by chetvern
File length: 20217 byte(s)
Diff to previous 44081

Moved more app args to lib (JIRA: GP-662)

Revision 44081 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Dec 7 18:27:39 2009 UTC (14 years, 5 months ago) by chetvern
File length: 18890 byte(s)
Diff to previous 44041

Process nested models explicitly

Revision 44041 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Dec 3 16:08:45 2009 UTC (14 years, 5 months ago) by chetvern
File length: 18736 byte(s)
Diff to previous 43989

Select finished chains separately by strands; sort chains by CDS limits

Revision 43989 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Nov 30 19:13:51 2009 UTC (14 years, 5 months ago) by chetvern
File length: 18432 byte(s)
Diff to previous 43913

Corrected model selection for prediction logic

Revision 43913 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Nov 19 20:22:15 2009 UTC (14 years, 6 months ago) by chetvern
File length: 17358 byte(s)
Diff to previous 43911

Fixed debug code

Revision 43911 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Nov 19 18:02:40 2009 UTC (14 years, 6 months ago) by chetvern
File length: 17343 byte(s)
Diff to previous 43906

annot_wnode app (JIRA: GP-663)

Revision 43906 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Nov 18 18:58:31 2009 UTC (14 years, 6 months ago) by chetvern
File length: 16707 byte(s)
Diff to previous 43877

Replaced functor with literal function for Sun's WorkShop compiler sake

Revision 43877 - (view) (download) (as text) (annotate) - [select for diffs]
Added Tue Nov 17 20:13:33 2009 UTC (14 years, 6 months ago) by chetvern
File length: 16793 byte(s)

Moved annot into library  (JIRA: GP-662)

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