adamewing/bamsurgeon — pull request #21 by andreaswilm (2014-12-15 07:24:46+00:00)
Title: Leading soft clips taken into account for insertions

- Fixes use of wrong insertion position when reads contain leading soft-clips (see pull request #19 for deletions).
- Number soft clips in both cases now determined through qstart instead of cigar operation.

Note, as you rightly pointed out: makeins() and makedel() should use aligned_pairs(). Not only is this more generic, but with this you would also avoid trouble with existing indels located before the mutation position (also messing up the calculation of that positions).