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@zhuchcn zhuchcn released this 21 Jun 06:04
· 439 commits to main since this release
v1.0.0
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Learn about vigilant mode.

Added

  • Added the support for calling peptides of Selenocysteine terminated. #684

  • Added the support for calling peptides of W > F codon reassignments. #484

  • Added the support for calling peptides with adjacent SNP/INDEL. #691

  • Updated fake.py and bruteForce to handle selenocysteine, W2F and MNV. #689

  • callAltTranslation added to call peptides with alternative translation without any genomic or transcriptomic variations.

  • Enabled summarizeFasta to create bar plot of the summary results.

Fixed

  • Fixed fake that simulated selenocysteine positions could be in introns.

  • Fixed fake that the last exon was picked for A3SS or first exon for A5SS.

  • Fixed fusion with very small intronic insertion. #707

  • In ThreeFrameTVG when aligning variant bubbles and when nodes are merged, variants were not merged correctly.

  • Fixed TVG that indel merged with downstream fusion treated as subgraph out. #708

  • Fixed parseRMATS to handle more complex situations such as exons interjacent between splicing sites and exons spanning over the splicing site. #715, #716, #717, and PR #720

  • Fixed callVariant that failed when there is a SNV very close to the end on a AltSplice insertion. #723

  • Fixed TranscriptAnnotationModel for not recognizing transcripts with mRNA_end_NF correctly. #724

  • Fixed callVariant issue of altSplice insertion carries an intronic indel that goes back to the original reading frame. #726

  • Fixed callVariant to handle deletion that spans over an entire intron. #732

  • Fixed callVariant to skip peptides earlier if they are either too long or too short to significantly improve efficiency. #736

  • Fixed callVariant to handle hypermutated region with a dynamic cutoff. #738

  • Fixed decoyFasta to make it as default to keep cleavage site amino acid residues unmodified. #750

  • Fixed SeqFeature and GTFSeqFeature to remove the definition of strand and use location.strand. #616

  • Refactored util so all functions are accessible. #749

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