Notable changes to pangene:
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Improvement: more aggressive pseudogene filtering. This helps the great ape graph.
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New feature: added option -E to filter out genes aligned with a single exon in all input genomes. Graphs constructed from multi-exon genes are usually cleaner.
Notable changes to pangene.js:
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Improvement (call): a new bubble finding algorithm via local graph traversal. Added a filter to remove falsely idenrified bubbles.
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New feature (call): output names of assemblies that support each allele.
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New feature: added the getaa subcommand to parse Ensembl and GenCode annotations.
(22 February 2024, r231)