bigdatagenomics/avocado — pull request #91 by fnothaft (2014-07-29 23:50:39+00:00)
Title: Adding fast aligner.

Adds a fast aligner to replace the HMM based aligner when scoring read alignments to haplotypes. There are two levels of fast aligner:

* A first, prefix trie-based fast aligner aligns reads that align perfectly or with a single mismatch
* A second fast aligner aligns reads that align with alignment matches

We try alignment with the first aligner; if this fails, we fall back to the second aligner.

This PR also removes the haplotypesFromReads variant caller.