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@zhuchcn zhuchcn released this 05 Oct 14:11
· 216 commits to main since this release
v1.2.1
8bb50b1
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Add

  • Added --graph-output-dir to save graph data in json.

Fixed

  • Fixed summarizeFasta that SEC and W2F on fusion peptides are ignored. #789

  • Fixed callVariant that variant_coordinates_to_gene failed when the deletion is end inclusion and it overlaps with the last nucleotide of an exon. #793

  • Fixed splitFasta that CodonReassign and SECT were not able to be grouped. #796

  • Fixed callVariant that in-frame subgraphs not recognized when they are not in variant bubble.

  • Fixed callVariant that peptides are falsely called if the last miscleaved node is missing a downstream cleavage altering variant. #800

  • Fixed TVGNode that get_max_subgraph_id always returns the last subgraph ID. #802

  • Fixed callVariant with altSplice insertion with intronic frameshift variant which is very closed to the end of the subgraph. #803

  • Fixed bruteForce that accepter variants are skipped if the donor transcript has variants with the same coordinate. #810

  • Fixed splitFasta that source and source group order gets overriden by GVF order. #805

  • Fixed summarizeFasta and splitFasta being too slow. #795

  • Fixed splitFasta to use top priority header for additional split

  • Fixed callVariant that some accepter only ORFs maybe included for noncoding fusion transcripts.

  • Fixed callVariant that when filtering variants for a given transcript/fusion/circRNA, coordinates of end inclusion insertions were not interpreted correctly.

  • Fixed bruteForce that selenocysteine not fixed for deletion alt sequence.

  • Fixed callVariant that nodes with fusion being treated as subgraph out or end node incorrectly.

  • Fixed callVariant that upstream cleavage altering variants were affecting checks for whether a node is hybrid in circRNA.

  • Fixed callVariant that two SNV at the same location in circRNA was affecting hybrid node identification.

  • Fixed callVariant. When creating the cleavage graph, when a variant bubble is processed, the downstream node(s) needs to be identified for the next iteration, and only in-frame node should be used. However some nodes can span over two reading frames, so we should check the last reading frame index instead of the first.

  • Fixed callVariant that accepter transcript variants very closed to the breakpoint were skipped.

Added

  • Added support for --group-source for summarizeFasta. #798
Assets 2