/[v1]/trunk/c++/src/sra/readers/bam/bamindex.cpp
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Revision 101886 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 28 18:12:53 2024 UTC (2 months ago) by vasilche
File length: 88685 byte(s)
Diff to previous 101493 
Use CByte_graph::TValues typedef. JIRA: OMDM-88
Revision 101493 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Dec 19 18:34:18 2023 UTC (4 months, 1 week ago) by vasilche
File length: 88677 byte(s)
Diff to previous 101436 
Do not include deprecated header <strstream>.
Revision 101436 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Dec 13 17:06:32 2023 UTC (4 months, 2 weeks ago) by vasilche
File length: 88699 byte(s)
Diff to previous 96857 
Allow explicit positioning within BAM file. JIRA: OMDM-67
Revision 96857 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu May 19 14:59:20 2022 UTC (23 months, 1 week ago) by vasilche
File length: 86779 byte(s)
Diff to previous 96759 
Fixed too far overlap in case of zero overlap and missing bin. JIRA: CXX-12408
Revision 96759 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 6 17:12:10 2022 UTC (23 months, 3 weeks ago) by vasilche
File length: 86528 byte(s)
Diff to previous 96678 
Fixed overlap calculation and alignment lookup for BAI/CSI indexes. Added tests for overlaps. JIRA: CXX-12408
Revision 96678 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 27 15:48:04 2022 UTC (2 years ago) by vasilche
File length: 78635 byte(s)
Diff to previous 96596 
Optimized alignment lookup. JIRA: CXX-12408
Revision 96596 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Apr 18 21:11:33 2022 UTC (2 years ago) by vasilche
File length: 74594 byte(s)
Diff to previous 96504 
Added configurable prefernce of CSI indexes. Fixed overlap calculation. JIRA: CXX-12408
Revision 96504 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Apr 7 22:40:27 2022 UTC (2 years ago) by vasilche
File length: 72226 byte(s)
Diff to previous 96503 
Fixed warning. JIRA: CXX-12408
Revision 96503 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Apr 7 22:26:20 2022 UTC (2 years ago) by vasilche
File length: 72217 byte(s)
Diff to previous 95002 
Implemented CSI index support. JIRA: CXX-12408
Revision 95002 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 27 16:36:44 2021 UTC (2 years, 7 months ago) by grichenk
File length: 68316 byte(s)
Diff to previous 92316 
Removed redundant CTempString. JIRA CXX-12115
Revision 92316 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jan 7 15:17:47 2021 UTC (3 years, 3 months ago) by vasilche
File length: 68331 byte(s)
Diff to previous 91393 
Avoid using deprecated strstream.
Revision 91393 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Oct 22 17:38:51 2020 UTC (3 years, 6 months ago) by grichenk
File length: 68540 byte(s)
Diff to previous 89360 
Replaced LOG_POST with ERR_POST. JIRA CXX-11086
Revision 89360 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 24 15:25:24 2020 UTC (4 years, 1 month ago) by vasilche
File length: 68540 byte(s)
Diff to previous 86746 
Implemented variable page size. JIRA: CXX-11011
Revision 86746 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 14 16:22:24 2019 UTC (4 years, 10 months ago) by vasilche
File length: 68472 byte(s)
Diff to previous 86745 
Fixed warning. JIRA: CXX-10702
Revision 86745 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 14 16:02:58 2019 UTC (4 years, 10 months ago) by vasilche
File length: 68462 byte(s)
Diff to previous 81464 
Optional addition of align aux tags. JIRA: CXX-10702
Revision 81464 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 5 17:30:54 2018 UTC (6 years, 1 month ago) by vasilche
File length: 65455 byte(s)
Diff to previous 80460 
Added option to omit cigars with ambiguous match. JIRA: CXX-9905
Revision 80460 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Dec 11 14:15:34 2017 UTC (6 years, 4 months ago) by gouriano
File length: 65085 byte(s)
Diff to previous 79606 
Added parsing of SAM header. JIRA: CXX-9744
Revision 79606 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 26 15:59:29 2017 UTC (6 years, 7 months ago) by vasilche
File length: 63762 byte(s)
Diff to previous 78515 
New pileup collector using SSE. Fixed some warnings. JIRA: CXX-9613
Revision 78515 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jun 26 19:07:04 2017 UTC (6 years, 10 months ago) by vasilche
File length: 63622 byte(s)
Diff to previous 78466 
Collect read times statistics. JIRA: CXX-9369
Revision 78466 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jun 22 14:09:20 2017 UTC (6 years, 10 months ago) by vasilche
File length: 62024 byte(s)
Diff to previous 78433 
Fixed file-range calculation for over-span alignements. JIRA: CXX-9350
Revision 78433 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 20 15:01:57 2017 UTC (6 years, 10 months ago) by vasilche
File length: 57509 byte(s)
Diff to previous 78370 
Added ESearchMode. Added filtering of unmapped reads. Fixed alignment to bin assignment. JIRA: CXX-9350
Revision 78370 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 13 18:38:38 2017 UTC (6 years, 10 months ago) by vasilche
File length: 56765 byte(s)
Diff to previous 78249 
Fixed alignment range limit calculation. JIRA: CXX-9350
Revision 78249 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jun 7 13:33:52 2017 UTC (6 years, 10 months ago) by vasilche
File length: 55985 byte(s)
Diff to previous 78212 
Added complementary GetAlnOverEnds(). Added proxy EstimateDataSizeByAlnStartPos(). JIRA: CXX-9285
Revision 78212 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 2 19:59:50 2017 UTC (6 years, 11 months ago) by vasilche
File length: 55516 byte(s)
Diff to previous 78172 
Implemented EstimateDataSizeByAlnStartPos(). JIRA: CXX-9285
Revision 78172 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed May 31 17:15:14 2017 UTC (6 years, 11 months ago) by vasilche
File length: 48563 byte(s)
Diff to previous 78141 
Fixed formatting of CIGAR string. Fixed linear index processing. JIRA: CXX-9285
Revision 78141 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 26 21:28:12 2017 UTC (6 years, 11 months ago) by vasilche
File length: 48338 byte(s)
Diff to previous 78075 
Implemented GetAlnOverStarts(). Added scaling info to coverage graph. Optimized index loading. JIRA: CXX-9285
Revision 78075 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue May 23 16:31:56 2017 UTC (6 years, 11 months ago) by vasilche
File length: 39563 byte(s)
Diff to previous 78013 
Fixed sequential scanning of whole BAM file. Added index-level requests for estimated graph. Added estimation information to the graphs. Added common test application argument parsing. JIRA: CXX-9285
Revision 78013 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu May 18 17:35:17 2017 UTC (6 years, 11 months ago) by vasilche
File length: 35981 byte(s)
Diff to previous 77893 
Define BAM index constants as enums to avoid linking problems. Added index-level requests. JIRA: CXX-9285
Revision 77893 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 12 14:58:02 2017 UTC (6 years, 11 months ago) by vasilche
File length: 33640 byte(s)
Diff to previous 77880 
MSVC 2013 doesn't support constexpt. JIRA: CXX-8325
Revision 77880 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu May 11 21:41:01 2017 UTC (6 years, 11 months ago) by vasilche
File length: 33511 byte(s)
Diff to previous 77223 
Optimized BAM loading via raw index access. JIRA: CXX-8325
Revision 77223 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Apr 3 20:58:27 2017 UTC (7 years ago) by vasilche
File length: 30643 byte(s)
Diff to previous 77207 
Renamed classes to avoid convlict with sraread library. Added raw CIGAR and read getters. JIRA: CXX-8325
Revision 77207 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Apr 3 14:57:42 2017 UTC (7 years ago) by vasilche
File length: 30586 byte(s)
Diff to previous 75483 
Implemented optional raw-index mode of CBamDb and its iterators. JIRA: CXX-8325
Revision 75483 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Nov 18 21:19:01 2016 UTC (7 years, 5 months ago) by vasilche
File length: 23994 byte(s)
Diff to previous 75398 
Implemented raw access graph generation. Removed header dependency on VDB Toolkit headers. JIRA: CXX-8325
Revision 75398 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Nov 14 20:36:00 2016 UTC (7 years, 5 months ago) by vasilche
File length: 23084 byte(s)
Diff to previous 75270 
Estimated graph generation without VDB BAM API. JIRA: CXX-8513
Revision 75270 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 1 19:37:50 2016 UTC (7 years, 6 months ago) by vasilche
File length: 24522 byte(s)
Diff to previous 75164 
Added reading of index file from remote locations. JIRA: CXX-8513
Revision 75164 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Oct 26 14:45:02 2016 UTC (7 years, 6 months ago) by vasilche
File length: 22239 byte(s)
Diff to previous 74428 
Added option to class CBam2Seq_graph and app bam2gaph to generate estimated graph. JIRA: CXX-8513
Revision 74428 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Aug 31 21:00:48 2016 UTC (7 years, 8 months ago) by vasilche
File length: 22078 byte(s)
Diff to previous 73442 
Added alignment flags. Fixed reading over EOF BGZG block. JIRA: CXX-8325
Revision 73442 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 7 19:13:27 2016 UTC (7 years, 9 months ago) by vasilche
File length: 20089 byte(s)
Diff to previous 73431 
Remove pseudo-bin. JIRA: CXX-8325
Revision 73431 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 7 15:24:17 2016 UTC (7 years, 9 months ago) by vasilche
File length: 19941 byte(s)
Diff to previous 73353 
Added MT-safety guards to CPagedFile. Allow additional gzip header extra fields. JIRA: CXX-8325
Revision 73353 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jun 30 21:34:51 2016 UTC (7 years, 10 months ago) by vasilche
File length: 19939 byte(s)
Diff to previous 73350 
Fixed warnings, optimized memory reallocations in Windows. JIRA: CXX-8325
Revision 73350 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jun 30 20:11:04 2016 UTC (7 years, 10 months ago) by vasilche
File length: 20283 byte(s)
Diff to previous 73241 
Added BGZF file reader and low-level BAM alignment iterator. JIRA: CXX-8325
Revision 73241 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 24 21:10:32 2016 UTC (7 years, 10 months ago) by vasilche
File length: 12299 byte(s)
Diff to previous 73240 
Fixed warnings. JIRA: GB-5917
Revision 73240 - (view) (download) (as text) (annotate) - [select for diffs]
Added Fri Jun 24 20:55:48 2016 UTC (7 years, 10 months ago) by vasilche
File length: 12282 byte(s) 
Added estimated graph generation. JIRA: GB-5917

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