e.g. , when pairtools flip --chroms-path hg38.reduced.chrom.sizes p1.pairs, where hg38.reduced.chrom.sizes does not have un-assembled contigs - it fails when encounters unrecognized name - e.g. KeyError: 'chrUn_KI270438v1'
in the same situation pairtools parse behaves differently - it flips what it can according to hg38.reduced.chrom.sizes and flips lexicographically everything else
no big deal - but we'd rather have it documented - to fix later
e.g. , when
pairtools flip --chroms-path hg38.reduced.chrom.sizes p1.pairs, wherehg38.reduced.chrom.sizesdoes not have un-assembled contigs - it fails when encounters unrecognized name - e.g.KeyError: 'chrUn_KI270438v1'in the same situation
pairtools parsebehaves differently - it flips what it can according tohg38.reduced.chrom.sizesand flips lexicographically everything elseno big deal - but we'd rather have it documented - to fix later