Fix the iteration over the CIGAR segments#1202
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daviesrob merged 1 commit intosamtools:developfrom Jan 15, 2021
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… indels, clips and skips, so that the next MATCH starts from 0 index. Co-authored-by: Valeriu Ohan <vo2@sanger.ac.uk>
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When encountering a new CIGAR segment, the index
icig, which indicates the position of a base inside the current segment, has to be reset. This fix changes the reset value to -1 (instead of 0), so that the next first matching base starts fromicig=0in the calling method (tweak_overlap_quality).Replaces #1196
Fixes #1195