Adding third column to bam types and remove name guessing.
--WARNING BAD TEMPORARY FIX WILL BREAK
Making the first input in spike_in_only mode the normal, the rest are tumors.
Changing defaults to match this particular set of exomes.
Reading libraries in even when spike_in_only is set
Revert "Reading libraries in even when spike_in_only is set"

This reverts commit 82f44fcd8c20cfef3074328634910ce2d5cb126e.
Changing from using global tumor bams to determining them from the list of mergedBams
Removing localizing BamFileNameCalculator dependencies to the fracture and merge stage.
Added "getName" to fix output directory.