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@zhuchcn zhuchcn released this 28 Jan 18:44
· 1372 commits to main since this release
v0.2.0
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Learn about vigilant mode.

This is the first unstable release of moPepGen, the graph based multi-omics peptide generator. Below is what got updated since v0.1.0-beta.1

Added

  • Multi-threading is enabled for callVariant to run in parallel.

  • CLI command indexGVF added to generate a index file for quickly access variant data from the corresponding GVF file. Noted that this command is not required to run.

Changed

  • To solve the complexity of subgraphs introduced by fusion and especially alternative splicing insertion and substitution, the SubgraphTree class is added to keep the graph-subgraph relationship between nodes.

  • Variant records are now kept on disk rather than reading the entire GVF file(s) into memory, and only the file pointers to variant records are kept in memory. This significantly reduces the memory usage of callVariant.

  • The command line arguments are standardized across all commands, for example '-i/--input-path' for inputs and '-o/--output-path' for outputs.

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