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Fixed warnings. JIRA OMDM-54
Address warnings affecting the consolidated seq library. - Do away with implicit narrowing conversions, which yield warnings under recent macOS and FreeBSD toolchains, mainly through a combination of type harmonization (including adjustments to some internal functions' signatures) and explicit casting. -- CDense_seg: Replace the usual sequence of consistency assertions with calls to a new ASSERT_CONSISTENCY macro, which does the same thing but on a pure size_t basis. - Use string::find when simply looking for a single case-sensitive character. - CReverseComplementHelper: Make fully empty, which has always been legitimate. - SeqTable_multi_data.cpp (sx_Round): Correctly detect values that are just too large for 64-bit integer types. JIRA: CXX-3707.
Fixed trimming gaps in mapped exons. JIRA CXX-12410
Invalidate scores when a segment can not be mapped. JIRA CXX-11958
Replaced autp_ptr with unique_ptr. JIRA CXX-11620
Smarter sequence type and length detection. JIRA CXX-7366
Optionally report any trimmed range as mapping error. JIRA CXX-7309
Skip empty segments in mapped std-seg. JIRA GP-14686
Fixed exon trimming for minus strand. JIRA CXX-6073
Copy seq-align::id to the mapped alignment. JIRA CXX-5968
Fixed possible null pointer usage. JIRA CXX-5700
Option to turn on/off gap trimming in spliced-seg. JIRA CXX-5691
Optionally convert mapped genome-to-protein alignment to spliced-seg. JIRA CXX-5478
Fixed gap trimming. JIRA CXX-5271
Trim insertions created by mapping. JIRA CXX-5259
Fixed exon splitting. JIRA CXX-5105
Fixed strand handling in spliced-segs. JIRA CXX-5105
Preserve product type when possible, throw when mapping product from protein to an unknown sequence type. JIRA CXX-5104
Fixed processing of indels in mapped alignments. Updated unit tests. JIRA CXX-4072
Trim indels only in the first/last exons. JIRA CXX-4072
Optimized initialization of CSeq_loc_Mapper_Base. JIRA CXX-4718
Fixed warning.
Use per-exon seq-ids if set. JIRA CXX-4503
Split exons mapped to multiple sequences - fix for genomic row. JIRA CXX-4432
Split exons mapped to multiple sequences. JIRA CXX-4432
Standardize protpos processing (JIRA: CXX-4415)
Fixed handling of duplicate mappings. JIRA CXX-4240
Do not try to map bounds through an empty mapper. JIRA CXX-4166
Remove gaps at exon start/end. JIRA CXX-4072
Throw CAnnotMapperException if the mapped alignment is empty. JIRA CXX-3970
Fixed partial flag in mapped exons. JIRA CXX-3817
Map spliced-seg bounds. JIRA CXX-3770
Do not sort exons and exon parts after mapping, use the original order. JIRA CXX-3770
Fixed mapping of spliced-segs. Reverted fix for mixed-strand alignments. JIRA CXX-3728, CXX-3666
Convert mixed strand mapped alignments into disc-segs. JIRA CXX-3666
Fixed product strand in mapped exons. JIRA CXX-3724
Fixed the order of segments when mapping through minus strand alignments. JIRA CXX-3666
Always preserve exon parts after mapping. Fixed processing of exons without parts in AsDiscSeg(). JIRA CXX-2993
Fixed spliced-seg mapping. JIRA CXX-2954
Fixed warnings.
Reverted changes made in r311310.
Fixed warnings.
Do not check product type of each exon in spliced-segs. JIRA CXX-1987
Fixed mapping of gaps in alignments. JIRA CXX-1966
Fixed sorting of mapped exon parts. Updated unit test. JIRA CXX-1806
Fixed sorting of mapped exon parts. JIRA CXX-1806
Fixed mapping of spliced segs with genomic location on minus strand. JIRA CXX-1663
Drop dense-segs with only gaps in some row. Fixed segfaults in seq-align mapper. Updated unit test. JIRA CXX-1603, CXX-1584
Fixed creation of partial dense-segs. JIRA CXX-1603
Fixed setting strands for gaps.
Added more comments. Minor fixes and improvements. Get additional sequence type hints from feature type. JIRA CXX-1584, CXX-1599.
Reversed indexing of spliced-seg rows. JIRA CXX-1555
Fixed order of parts in mapped exons. JIRA CXX-1530
Fixed missing seq-ids in exons which contain only gaps for genomic or product sequence. JIRA CXX-1491
Fixed list sorting for Workshop. JIRA CXX-1491
Fixed sorting of exon parts and seq-id assignment in exons. JIRA CXX-1491
Fixed calculation of segment length in std-segs. JIRA SB-473
Modified Seq-loc and Seq-align mappers to use only genomic coordinates internally. JIRA CXX-1344
Fixed mapping of exons - split exon on segment boundaries. JIRA CXX-1336
Fixed processing of scores: remove scores if any related segment is truncated. JIRA CXX-1328
Fixed handling of scores in dense-segs. JIRA CXX-1287
Fixed creation of disc aligns for multi-id mapped alignments. JIRA CXX-1287
Fixed mapping through spliced-seg -- take exon parts into account. JIRA CXX-1284
Fixed splitting mapped alignment into dense-segs. JIRA CXX-1287
Fixed copying of data to mapped alignments. JIRA CXX-776
Fixed mapping of Spliced-seg alignments. Updated unit tests. JIRA CXX-776
Do not set product-length in mapped spliced-segs. JIRA CXX-1151
Fixed mapping of frames. JIRA CXX-1138
Fixed mapping of Spliced-seg parts, updated unit test. JIRA CXX-776
Fixed alignment row truncation.
Fixed bug in width mapping.
Throw exception if a mapped denseg row contains only gaps. Skip invalid sub-alignments in disc. Fixed warnings. JIRA CXX-665
Throw exception on inconsistent segment length. JIRA CXX-654
Warn about wrong segment length in std-seg. JIRA CXX-654
Fixed calculation of segment length in mixed std-seg with gaps. JIRA SB-100, CXX-654
Fixed problem with segment length in std seg. JIRA SB-100
Move error_codes.hpp from objects/ to objects/misc directory to allow make external references to separate objects/ subdirectories.
Fixed mapping of dense-segs between nucs and prots.
Fixed warnings.
Added support for spliced and sparse alignments in mappers and OM. CXX-201
Added undef of NCBI_USE_ERRCODE_X because these files can be compiled simultaneously by including into one source. JIRA: CXX-3
Objects and objmgr libraries are changed for new error and log posting system. JIRA: CXX-3
Fixed mapping of gaps and multi-id rows.
Fixed svn properties in trunk/c++.
CVS $Log$ keyword clean-up: everything except "internal".
Allow to map a single row rather than whole alignment.
Fixed mapping of CSeq-align objects.
Initial revision
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