bigdatagenomics/adam — pull request #129 by fnothaft (2014-02-21 23:18:23+00:00)
Title: Modified pileup transforms to improve performance + to add options

This change came up when working on #121:

* Removed two unnecessary count operations during pileup conversion that negatively impacted performance.
* Added a switch to all pileup conversions (both pileup and rod) to specify whether reads that are at non-primary mappings should be converted into pileups. By default, we only convert primary mappings.