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Expose gene ID lookup by bioseq handle with no alignment JIRA GP-37532
Fallback for getting geneID; if DBXref not found, use LocusID from data.db JIRA GP-37532
Introduce new filter predicate: query_subject_overlap JIRA: PGAP-9042
new tokens for query and subject species JIRA GP-35725
Fix issues with computation of Shannon's entropy for proteins. Expose Shannon's entropy and seg_pct as both alignment filter options and as tabular format options JIRA: PGAP-6650
Take product strand into account for poly-a score JIRA GP-30785
More code to use TTaxId. JIRA CXX-10489
New align_format and align_filter tokens JIRA GP-28521
Bug in counting non-frame indels for a row JIRA GP-27659
Clarify help text for gap and frameshift tokens JIRA GP-27726
New tokens for counting non-frameshift indels JIRA GP-27659
If polya is not found, value is 0 rather than NULL JIRA GP-24596
New tokens for subject coverage JIRA GP-20257
polya token JIRA GP-3086
Add checks around proper retrieval of sequences JIRA: GP-19440
When calculating frameshifts, no need to look up Bioseq for protein alignments JIRA GP-19440
frameshift count should only include frameshifts within cdregion JIRA GP-19371
* Make CBioseq's CSeq_loc-based constructor explicit, resolving ambiguity errors between GetId variants in some configurations. * When constructing a CSeqVector from a CSeq_loc, make sure to pass the scope by "value" (really C++ reference) rather than pointer (or CRef), as the latter approach inadvertantly relied on implicit "conversion" to CBioseq. JIRA: CXX-7746.
JIRA: GP-11703: Score Lookup can use CScoreBuilder Tie Breaker
BLAST score ration changes to make the ratio symmetric
support protein-to-nucleotide alignments (JIRA: GP-10572)
Avoid crash when gene feature has no gene id
Allow comma as a delimiter JIRA: GP-9069
min_indel_to_splice token JIRA GP-4527
New query_geneid and subject_geneid tokens JIRA GP-4527
Fix compilation warnings
Use new internal stops finder (JIRA: GP-6216)
Standardize protpos processing (JIRA: CXX-4415)
When counting internal stops, translate CDS region over collected mRNA instead of genome, in order to correctly handle frameshifts JIRA GP-4027
Remove code-breaks introduced by CFeatureGenerator before counting internal stops JIRA GP-4027
null value for 5/3exon tokens for spliced-seg unspliced alignment JIRA GP-1368
New tokens for 5prime and 3prime exons JIRA GP-1368
To look for internal stops, translate CDS Seq-feat rather than just its location, so frame is taken into account JIRA GP-3105
Use taxonomy fast-path lookup
Fix bugs in the detection of start and stop codons; correctly handle origin-crossing alignments JIRA GP-2797
Revise implementation of start/stop codon detection JIRA: GP-2552, GP-2544
Always CFeatureGenerator for translating cds JIRA GP-2468
Use correct genetic code for genomic sequence when computing cds_internal_stops, start_codon and stop_codon scores JIRA GP-2374
Generalize start_codon/stop_codon to non-spliced alignment types; don't unnecessarily use CFea tureGenerator for protein alignments JIRA GP-2258
Compute start_codon and stop_codon values if it is not pre-computed JIRA GP-2258
When filtering on a AND or OR expression, do the easy nodes first JIRA GP-2188
Remove try/catch logic from CScoreBuilderBase. Added a configurable error mode. Default is to report, but later, will be changed to throw. JIRA: GP-2125.
symmetric_overlap adjustment: handle protein-protein alignments correctly JIRA: GP-1917
Bug fixes for Splcied-seg protein-to-genomic BLAST score
Add interface to compute tBLASTn score for ProSplign Spliced-seg alignments JIRA: GP-1759
JIRA GP-1710 add start_codon and stop_codon keywords
JIRA GP-1692 Function for counting frame-shifts in an alignment
JIRA GP-1610 correct handling of exception thrown when computing the symmetric_overlap scores, and handling of protein sequences
JIRA GP-1610 symmetric_overlap_min score, calculating percent coverage over shorter of sequences
JIRA GP-1653 Constistently throw exception if score is not found or can't be calculated; handling is up to caller
JIRA GP-1653 fix typo
JIRA GP-1653 Add general check for integer vs. real-value scores
fix compilation warning on some platforms
JIRA GP-1653 fix bug in help text for unsupported score names
JIRA GP-1653 Make CScoreLookup a subclass of CScoreBuilder
JIRA GP-1653 refactor extraction and computation of alignment scores and computed tokens into new class, CScoreLookup
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