bigdatagenomics/avocado — pull request #49 by fnothaft (2014-04-21 04:35:00+00:00)
Title: Fixes to HMM/Haplotype code to correct indel calling.

This pull request makes several fixes to correct short indel calling. Additionally, we eliminate extra state which was kept around during the HMM alignment process, which improves the efficiency of the HMM aligner.