Aligned Bam Result: add bam_file as output; add flagstat calculation on output bam
Merged Alignment Result: is now AlignedBamResult; add is_output to bam_file
Alignment Result: is now AlignedBamResult
GATK Inst Data Indel Realigner Result
InstData GATK: add test module w/ ref and bam for testing
InstData GATK: indel realigner uses test module
InstData Gatk: add known indels to Test.pm
InstData Gatk: add base with known indels class
InstData Gatk: mv prepare output dir to base class
InstData Gatk: rm prepare output dir and known indels from indel realigner and make the class inherit from base with known indels
InstData Gatk: add version to base and indel realigner
InstData Gatk: indel realigner test uses known indels
InstData Aligned Bam: add bam_flagstat_file
InstData Gatk: indel realigner test compares intervals file and flagstat
InstData Gatk: add base recalibrator
GMT GATK Print Reads: rename bai to match samtools standard
InstData Gatk: add comments to tests
InstData Gatk: remove result from names to make the commands with saved results
InstData Gatk: remove Result from class names
Revert "InstData Gatk: remove Result from class names"

This reverts commit 5d2b1d5112b4ae9f20f6dc01c4b7c71a776afae6.