BenLangmead/bowtie2 — pull request #10 by jeffhussmann (2014-09-08 14:23:18+00:00)
Title: accounts for soft-clipping in DP redundancy checks

When calculating the coordinates of the dynamic programming cells that an alignment consists of, the current code does not take soft clipping into account. This means that, when the --local and --all flags are set, different portions of a read that align to the same stretch of a reference sequence are considered redundant and only one is reported.

To fix this, this pull request changes the calculation of these coordinates to use absolute positions in a read rather than positions relative to the first aligned base.

(The use case that revealed this behavior is when reads consist of concatamers, as in http://www.pnas.org/content/110/49/19872.abstract.)