Fix _longest_orf partialStart initialization and boundary condition - #11
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May 23, 2026 06:26
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This PR fixes a bug in
_longest_orfwherepartialStartandpartialStoparrays were not properly initialized when returning an mRNA CDS or when falling back, causing aSystemExit(1)error during length validation ingff2dict(e.g.ERROR in parsing gene gapmm2_4).It also fixes an off-by-one boundary bug (
cov < lenOrfinstead ofcov <= lenOrf) which caused it to over-extend the CDS when its length perfectly matches the required ORF coverage.This fixes the issue reported in
funannotate2#44where transcript alignments withgapmm2crash the parsing phase.Pull Request opened by Augment Code with guidance from the PR author