Revert "Revert lumpy commits until we figure it out"

This reverts commit a7cfb3881105a671e43e81e56aea459b5885f847.
perltidy and other minor cleanup
refactor _detect_variants and bam_split subroutines
Refactor paired end bam processing
refactor of split read processing
Refactor parameter parsing
Slight refactor of lumpy script handling
calculate read length from bam file instead of hardcoding it
version test data
programatically set the id for the lumpy pe and sr parameters
GMT GATK: make known sites optional