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Release 0.10.0
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@zhuchcn zhuchcn released this 20 Oct 17:14
· 940 commits to main since this release
v0.10.0
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Added

  • Added support for fusion, alternative splicing and circRNA in bruteForce.

Fixed

  • Several issues of bruteForce were fixed for fusion, alternative splicing and circRNA to be consistent with callVariant.

  • In ThreeFrameTVG and PeptideVariantGraph, large deletions (for alternative splicing) are no longer treated as subgraphs any more.

  • Fixed the issue that the subgraph_id attributes of TVGNode and PVGNode are lost after nodes are merged. #566

  • When expanding the aligned variant bubble, if the downstream node of the start node has multiple inbond nodes, nucleotides will be taken from the downstream node and added to each upstreams

  • Fixed callVariant that when filtering variants that are compatible with fusion, the breakpoint site were not recognized correctly. #567

  • For `ThreeFrameTVG', when aligning variant bubbles, if the end of the first variant is the start of the next (e.g. alternative splicing events that sharing the same splicing site), the merged bubble will then contain both variants

  • Fixed callVariant that mutations are assigned as stop altering mutation when there is a start codon after it. #568

  • Fixed callVariant that alternative splicing variants were not recognized as stop altering mutation correctly because their reference sequence from GVF is only the first nucleotide. #569

  • Fixed callVariant that nodes being lost after an in-frame subgraph. #573

  • Fixed callVariant that the actual fusion breakpoint was not found correctly when trying to tell whether a novel start site should be considered.

  • Fixed callVariant that variant peptides were called with variants present in one loop but not in another. #576

  • When collapsing the end nodes when creating the peptide cleavage graph, nodes that contains alt splice deletions are now separated from others. #580

  • Fusion not inserted correctly when the breakpoint is intronic. #578

  • When finding start altering variants from a node, wrong right position was used. #583

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