- Added --skip-failed flag to callVariant, parseArriba, parserSTARFusion, parseFusionCatcher.
- Added tally table to parseREDITools, parseCIRCExplorer, and parseRMATS
1.4.6rc2
Fixed
- Fixed callVariant that variant bubble not identified correctly.
- Fixed parseVEP that failed records will now be skipped with --skip-failed. 902
- Fixed callVariant with variant bubble finding error starting from a out-bridge node.
- Fixed callVariant that peptide annotation not created correctly with SEC
Changed
- A check added when converting a genomic location to gene coordinate to ensure they overlap.
1.4.6rc1
Fixed
- Fix callVariant for a case that a bridge-out node was not identified correctly with a lot of framshift variants.
1.4.5
Fixed
- Variant peptide not split correclty if it is derived from fusion that the upstream and downstream are the same gene. 897
1.4.4
Fixed
- Fixed issue reported in 889 where variant bubbles alignment failed due to incorrect handling of in-bridge and out-bridge nodes with the same subgraph ID. The fix ensures that only in-bridge and out-bridge nodes connected to any of the nodes in the members of the variant bubble are considered.
- Fixed issue that `callVariant` fails on transcripts with SEC very close to the start codon.
- Fixed issue with extremely long run-time with complex alt splice events. 892
1.4.3
Fixed
- Fixed `VariantPeptideIdentifier` that ORF ID was added before variant IDs.
- Fixed `callVariant` that failed on small circRNA with a lot of variants at the step that creates the cleavage graph. 885
- Fixed `fuzzTest`. Parameters missing for `callVariant`.
Changed
- Changed variant IDs for circRNAs to use backsplicing site instead of listing all exons/introns. 878