* removed references to old picard style genome reference and just use internal GATK methods
* fixes for breaks from latest GATK
* fixed breaks due to GATK change -- Pileup now requires read pile to be sorted upon construction
* formatting changes so -0 is output as 0
* refactoring to fragment based pileups
* refactoring to fragment based pileups... and made it faster
* removal of simulation code
* added filter to remove reads with XT:M tag (mapped due solely to mate pair)
* fixed filter to remove reads with XT:M tag (mapped due solely to mate pair)
* made sequencing error model public enum
* attempt to use BAQ in t2 read pile
* parameterize BAQ
* refactored call stats output to separate class
* implemented strand power calculations
* implemented normal artifact power calculation
* added @Output to various coverage files so they play nicer with Queue
* fixed bug in tumor power calculation for case lodThreshold == 0
* fixed serious bug in contamination lod calculation which caused all contamination lods == 0
* workaround of GATK issue that requires ReadBackedPileups to be stratified by sample (which I don't want for the simulator!)
* regretting overzealous commit
* normal_artifact_lod was getting triggered when we were running without a matched normal.  fixed
* fixed bug in normal power calculation for case lodThreshold == 0
* moved to LOCUS partitioning for Queue -- should improve throughput by evenly chopping up jobs by readcount