The previous version didn't do overlap removal for deletions, meaning we'd get the same read twice where one copy had a deletion.
This is still true for more complex compound cigar strings as 2M1I5D1I5M in the second record. Possibly this can be improved on further[*], but it's a pretty exotic case that is unlikely to cause problems and the behaviour in this PR there is the same as how it used to be (ie it falls back to the old method of just continuing to the next position).
Fixes samtools/samtools#1992
[*] The cause of 5D1I5M failing is because we're on the "M" cigar and the previous is not "D". We could relax that check, but I wasn't confident this would work in all possible scenarios, eg backwards B skips or N ref-skips.
The previous version didn't do overlap removal for deletions, meaning we'd get the same read twice where one copy had a deletion.
This is still true for more complex compound cigar strings as
2M1I5D1I5Min the second record. Possibly this can be improved on further[*], but it's a pretty exotic case that is unlikely to cause problems and the behaviour in this PR there is the same as how it used to be (ie it falls back to the old method of just continuing to the next position).Fixes samtools/samtools#1992
[*] The cause of 5D1I5M failing is because we're on the "M" cigar and the previous is not "D". We could relax that check, but I wasn't confident this would work in all possible scenarios, eg backwards B skips or N ref-skips.