Fix tai index lookup bug for incomplete chroms

ComparativeGenomicsToolkit / taffy

This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files

MIT License

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Fix tai index lookup bug for incomplete chroms #29

Closed glennhickey closed 1 year ago

glennhickey commented 1 year ago

Just noticed that .tai region queries were not working correctly on reference chromosomes that are only partially represented in the alignment. This is a case that now happens when, say, hardmasked gaps are filtered out of the MAF before indexing.