[v1] Log of /trunk/c++/src/sra/readers/sra/snpread.cpp

Revision 100333 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 20 14:36:26 2023 UTC (9 months, 1 week ago) by vasilche
File length: 87293 byte(s)
Diff to previous 100249

Removed obsolete constant (it's in another file now). JIRA: OMDM-51

Revision 100249 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jul 12 17:50:46 2023 UTC (9 months, 3 weeks ago) by vasilche
File length: 87338 byte(s)
Diff to previous 100244

Fixed MSVC conversion warning. JIRA: OMDM-49

Revision 100244 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jul 12 15:04:46 2023 UTC (9 months, 3 weeks ago) by vasilche
File length: 87324 byte(s)
Diff to previous 100229

Added entry generation API. JIRA: OMDM-49

Revision 100229 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jul 11 13:37:53 2023 UTC (9 months, 3 weeks ago) by vasilche
File length: 85380 byte(s)
Diff to previous 97025

Added split/chunk generation API. JIRA: OMDM-49

Revision 97025 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jun 9 14:24:56 2022 UTC (22 months, 3 weeks ago) by vasilche
File length: 75759 byte(s)
Diff to previous 96353

Reduce number of GetRequestContext() calls. JIRA: CXX-12491

Revision 96353 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Mar 18 13:54:22 2022 UTC (2 years, 1 month ago) by vasilche
File length: 75514 byte(s)
Diff to previous 85407

Made sraread library not dependent on OM. JIRA: CXX-12402

Revision 85407 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Feb 7 20:03:37 2019 UTC (5 years, 2 months ago) by vasilche
File length: 78519 byte(s)
Diff to previous 85122

Fixed race condition in loading sequence SNP parameters. JIRA: CXX-10464

Revision 85122 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jan 16 17:13:49 2019 UTC (5 years, 3 months ago) by vasilche
File length: 78279 byte(s)
Diff to previous 84458

Removed debug messages. JIRA: CXX-10428

Revision 84458 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Nov 9 23:29:50 2018 UTC (5 years, 5 months ago) by vasilche
File length: 78490 byte(s)
Diff to previous 83719

Fixed sequence lookup by index. JIRA: CXX-10231

Revision 83719 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 12 21:08:18 2018 UTC (5 years, 7 months ago) by vasilche
File length: 78431 byte(s)
Diff to previous 83718

Properly upcase both versions of ACCESSION. JIRA: CXX-10231

Revision 83718 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 12 19:16:26 2018 UTC (5 years, 7 months ago) by vasilche
File length: 78532 byte(s)
Diff to previous 83702

Try both ACC.1 and ACC.001 versions for compatibility with old VDB files. JIRA: CXX-10229

Revision 83702 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 11 22:39:52 2018 UTC (5 years, 7 months ago) by vasilche
File length: 78276 byte(s)
Diff to previous 76879

Optimized opening of SNP VDB file with large number of sequences. Added workaround for PAGE to FEAT pointer error in VDB data. JIRA: CXX-10231

Revision 76879 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Mar 10 00:00:49 2017 UTC (7 years, 1 month ago) by vasilche
File length: 72777 byte(s)
Diff to previous 76315

Added zoom level getters. JIRA: CXX-8204

Revision 76315 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 31 17:43:07 2017 UTC (7 years, 3 months ago) by vasilche
File length: 72615 byte(s)
Diff to previous 75478

CSafeFlags is completely compatible with int. JIRA: CXX-9086

Revision 75478 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Nov 18 18:25:23 2016 UTC (7 years, 5 months ago) by vasilche
File length: 72626 byte(s)
Diff to previous 75363

Removed header dependency on VDB Toolkit headers. JIRA: JIRA: CXX-8291

Revision 75363 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Nov 9 16:43:35 2016 UTC (7 years, 5 months ago) by vasilche
File length: 72578 byte(s)
Diff to previous 75214

Added enum and getters for SNP subtype identification string. JIRA: CXX-8291

Revision 75214 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Oct 28 18:23:25 2016 UTC (7 years, 6 months ago) by vasilche
File length: 72661 byte(s)
Diff to previous 75108

Changed value to represent inversion variation subtype. JIRA: CXX-8291

Revision 75108 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Oct 20 19:44:29 2016 UTC (7 years, 6 months ago) by vasilche
File length: 72661 byte(s)
Diff to previous 74845

Added variation subtype, renamed QualityCodes to Bitfield. JIRA: CXX-8291

Revision 74845 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Sep 29 17:27:24 2016 UTC (7 years, 7 months ago) by vasilche
File length: 71028 byte(s)
Diff to previous 74648

Removed obsolete constants. JIRA: CXX-8291

Revision 74648 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 19 15:54:27 2016 UTC (7 years, 7 months ago) by vasilche
File length: 71106 byte(s)
Diff to previous 74630

Represet insertion SNPs with symmetric location. JIRA: CXX-8291

Revision 74630 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Sep 16 22:11:37 2016 UTC (7 years, 7 months ago) by vasilche
File length: 71170 byte(s)
Diff to previous 74611

Added option for no-gaps in graphs. JIRA: CXX-8291

Revision 74611 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Sep 15 17:12:15 2016 UTC (7 years, 7 months ago) by vasilche
File length: 70479 byte(s)
Diff to previous 74413

Set length 1 to insertions (len==0). JIRA: CXX-8291

Revision 74413 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Aug 31 15:37:13 2016 UTC (7 years, 8 months ago) by vasilche
File length: 70393 byte(s)
Diff to previous 74397

Use track graph to optimize filtered feature lookup. JIRA: CXX-8291

Revision 74397 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Aug 30 18:36:23 2016 UTC (7 years, 8 months ago) by vasilche
File length: 68299 byte(s)
Diff to previous 74382

Unified coverage and overview graph collection. JIRA: CXX-8291

Revision 74382 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Aug 29 22:47:54 2016 UTC (7 years, 8 months ago) by vasilche
File length: 73254 byte(s)
Diff to previous 74381

Fixed warnings. JIRA: CXX-8291

Revision 74381 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Aug 29 22:39:33 2016 UTC (7 years, 8 months ago) by vasilche
File length: 73241 byte(s)
Diff to previous 74323

Fixed generation of coverage graph on odd ranges. Added test for correct coverage graph. JIRA: CXX-8291

Revision 74323 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Aug 24 21:15:42 2016 UTC (7 years, 8 months ago) by vasilche
File length: 70184 byte(s)
Diff to previous 74322

Fixed warnings. JIRA: CXX-8291

Revision 74322 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Aug 24 20:56:08 2016 UTC (7 years, 8 months ago) by vasilche
File length: 69971 byte(s)
Diff to previous 72972

SNP VDB reader updated to schema with filtered tracks. JIRA: CXX-8291

Revision 72972 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 10 16:37:32 2016 UTC (7 years, 10 months ago) by vasilche
File length: 56189 byte(s)
Diff to previous 72761

Use sat/satkey as blob id. JIRA: CXX-8209

Revision 72761 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu May 26 16:54:41 2016 UTC (7 years, 11 months ago) by vasilche
File length: 55356 byte(s)
Diff to previous 72433

Fixed name of feature table. JIRA: CXX-7944

Revision 72433 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 6 19:38:05 2016 UTC (7 years, 11 months ago) by vasilche
File length: 55357 byte(s)
Diff to previous 72427

Added SNP coverage graphs. JIRA: CXX-7944

Revision 72427 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 6 13:44:35 2016 UTC (7 years, 11 months ago) by vasilche
File length: 54752 byte(s)
Diff to previous 72303

Implemented splitting of SNP annots. JIRA: CXX-7944

Revision 72303 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Apr 28 21:56:50 2016 UTC (8 years ago) by vasilche
File length: 52688 byte(s)
Diff to previous 72187

Use separate string list to avoid CTempString() data loss. JIRA: CXX-6242

Revision 72187 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 20 20:55:58 2016 UTC (8 years ago) by vasilche
File length: 52604 byte(s)
Diff to previous 72163

Fixed sparse index generation. Added information about sorted locations. JIRA: CXX-6242

Revision 72163 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Apr 19 16:20:08 2016 UTC (8 years ago) by vasilche
File length: 49848 byte(s)
Diff to previous 72097

Added CSafeFlags<> template for concept testing. JIRA: CXX-6242

Revision 72097 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Apr 14 19:22:17 2016 UTC (8 years ago) by vasilche
File length: 49839 byte(s)
Diff to previous 72001

Made methods non-inline to avoid extra header dependency. JIRA: CXX-6242

Revision 72001 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Apr 11 16:10:28 2016 UTC (8 years ago) by vasilche
File length: 49044 byte(s)
Diff to previous 72000

Removed noexcept. JIRA: CXX-6242.

Revision 72000 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Apr 11 15:59:55 2016 UTC (8 years ago) by vasilche
File length: 49053 byte(s)
Diff to previous 71920

Implemented separate allele columns. Split tables by set of columns. JIRA: CXX-6242

Revision 71920 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 6 18:33:20 2016 UTC (8 years ago) by vasilche
File length: 43421 byte(s)
Diff to previous 71687

Replaced deprecated Tokenize() calls.

Revision 71687 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 22 21:51:23 2016 UTC (8 years, 1 month ago) by vasilche
File length: 43293 byte(s)
Diff to previous 71685

Use <unordered_map>. JIRA: CXX-6242

Revision 71685 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 22 21:24:44 2016 UTC (8 years, 1 month ago) by vasilche
File length: 43290 byte(s)
Diff to previous 71680

Implemented filtering. JIRA: CXX-6242

Revision 71680 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 22 19:49:09 2016 UTC (8 years, 1 month ago) by vasilche
File length: 42969 byte(s)
Diff to previous 69597

Updated to 64-bit flags, added flag filtering API, produce Seq-table. JIRA: CXX-6242

Revision 69597 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Nov 2 17:54:49 2015 UTC (8 years, 6 months ago) by vasilche
File length: 35555 byte(s)
Diff to previous 69550

Added SNP table loading. JIRA: CXX-6242

Revision 69550 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Oct 29 17:18:43 2015 UTC (8 years, 6 months ago) by vasilche
File length: 31810 byte(s)
Diff to previous 69548

Added coverage graph generation. JIRA: CXX-6242

Revision 69548 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Oct 29 15:36:48 2015 UTC (8 years, 6 months ago) by vasilche
File length: 27070 byte(s)
Diff to previous 69532

Allow SNP reader to be called with non-SNP accession (e.g. VDB graph).
Added coverage graph getters. JIRA: CXX-6242

Revision 69532 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Oct 28 17:34:41 2015 UTC (8 years, 6 months ago) by vasilche
File length: 24232 byte(s)
Diff to previous 68642

Updated to new SNP schema and implemented query by range. JIRA: CXX-6242

Revision 68642 - (view) (download) (as text) (annotate) - [select for diffs]
Added Thu Aug 20 19:37:47 2015 UTC (8 years, 8 months ago) by vasilche
File length: 14907 byte(s)

Initial implementation of VDB SNP reader. JIRA: CXX-6242

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