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@zhuchcn zhuchcn released this 28 Jan 19:35
· 734 commits to main since this release
v0.11.0
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Fixed

  • When filtering variants for circRNA, those on fragments that are shorter than 3 nucleotides will not be included. #613

  • When collapsing nodes with the same sequence, global variants (mostly circRNA) are no longer considered when comparing variants, so that nodes with no other variant won't be discarded mistakenly. #619

  • Fixed issue that for hybrid nodes that span over a junction site on a circRNA, the location got lost and caused it to fail to identify whether the node is at least one loop downstream to an ORF start site. #621

  • Fixed issue that circRNA with only 1 nucleotide was causing it to fail to filter variants. #623

  • Fixed issue that peptide nodes on different subgraphs were collapsed after expanding the variant bubble, causing downstream nodes to be unprocessed and resulting in * in the final sequences. #625

  • Fixed issue that the ORF start site position cannot be interpreted when checking whether it is at least one loop away, because it can be off by 1 when converting the location from the gene coordinate to amino acid. #630

  • Fixed issue that the 'CHROM' attribute of GVF metadata not read in correctly. #629

  • Fixed issue that when a frameshift insertion is on a alt splice frameshift substitution (or insertion), the node became disconnected after aligning the variant bubble. #635

  • Fixed issue that when getting the stop altering mutations, location comparison was done incorrectly by 1. #636

  • Node in circRNA missing downstream stop lost mutation called as variant peptide incorrectly. #637

  • Silent mutation not excluded when it is very closed to anther mutation. #638

  • Stop retaining mutation not excluded. #638

  • Fusion with donor breakpoint smaller than 3 causing it fail to run. #633

  • Alt splice insertion recognized as stop altering incorrectly. #640

  • Fix that variants that overlap with last 3 nucleotides of the transcripts causing it to fail. #645

  • Fixed parseREDItools that the ref and alt nucleotides were not set correctly for negative strands. #644

  • Fixed callVariant that hybrid peptide sequences were called from circRNA. #653

  • Fixed callVariant that peptides with variants of in-frame mutation causing deletion/insertion between two cleavage sites were missed. #655

  • Fixed callVariant that when setting the max number of variants per peptide, the number of miscleavages was not used correctly. #657

Changed

  • The transcript trailing peptides (peptides at the end of the transcript sequence) are now excluded for transcripts with the mRNA_end_NF tag and circRNA regardless of it. Otherwise for transcripts (either coding or noncoding) that the mRNA end is confirmed (without the mRNA_end_NF) they are now included in the final FASTA. #649

  • Change from ray back to pathos for parallelization. #643

  • Gene ID of the transcript from which a noncoding peptide is called is added to the FASTA header. #662

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