[avocado-125] Move to new alignment loader.
Merge pull request #126 from fnothaft/change-loader

[avocado-125] Move to new alignment loader.
Making some filter().size() calls into .count()'s
[avocado-114] Mutect implementation.

Initial commit contains the implementations of read pre-processing and
filters for tumor and normal sample reads.
Adding the Mutect probabilistic models.
Fixing the compilation errors, back outline for Mutect caller.