Hotfix for transcript projection onto haplotypes with tandem duplications in vg rna #4397
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Changelog Entry
To be copied to the draft changelog by merger:
vg rnanow excludes haplotypes with tandem duplications when projecting rather than crashing on themDescription
This is a less-than-ideal solution to the problem since it leads to loss of some haplotype-specific transcripts, but it's an improvement over the current behavior, which is to crash on a failing assert. A better solution will be to always build the R-index alongside the GBWT so that we can get reachability information from locate queries. This will require some more pipeline engineering in
vg rnaandvg autoindex.