Calculates the ref length of mate read using "MC:Z" when available #67
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Previously, we inferred the mate reference length using the query length of a read. This can result in inconsistent lift-over results between a pair of reads. For example, if the soft clipped region of a paired-end read overlaps with a chain gap, leviosam2 used to ignore the gap for the main segment but assign the mate to be unliftable.
The
MC:Ztag describes the CIGAR of the mate read in the paired-end mode. This PR uses the tag (when available) to calculate the mate starting and ending positions (wrt the reference) to increase the consistency of paired-end lift-over.This feature is not compatible with htslib v1.11, which is pretty old. I also terminate the support of that version in this PR.