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Description
Currently looking up a chromosome not found in the index of a file croaks with an error in Indexes.overlapchunks because seqid has a value of Nothing. Error is not captured with if condition:
function overlapchunks(tabix::Tabix, interval::Interval)
seqid = findfirst(isequal(BioGenerics.seqname(interval)), tabix.names)
if seqid == 0
throw(ArgumentError("failed to find sequence name '$(BioGenerics.seqname(interval))'"))
end
return overlapchunks(tabix.index, seqid, BioGenerics.leftposition(interval):BioGenerics.rightposition(interval))
end
Suggest to change handling of this situation altogether. In a situation where the chromosome is not found in the tabix.name function should return an empty list of chunks. This would be useful when handling sex chromosomes in a more natural way (just like tabix utility does).
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