adamewing/bamsurgeon — pull request #19 by andreaswilm (2014-12-12 09:46:00+00:00)
Title: Fixed handling of leading clip when inserting deletions

Leading soft clips (e.g. 5S95M) are not taken into account when introducing deletions into reads. Consequently the deletion positions within the reads are off. This will ultimately lead to false, low frequency deletions inclose to introduced deletions.

This pull request fixes the behaviour for deletions. Insertions are very likely affected the same way, which can be fixed in a similar fashion.
Andreas

PS: Test case available on request.