Can't filter on subclass now that we have an abstract parent class for merged results.
Refine Read GATK: base recalibrator is now base recalibrator bam result
InstData Merge: create refiner command then call shortcut/execute
InstData Aligned Bam Result: rename bam_file to bam_path
SomVal: use bam_path instead of merged_alignment_bam_path in align reads
InstData GATK: add inst data property to base
InstData Aligned Bam: add bam_file alias
Inst Data Refine Reads Gatk: use indel realigner as bam, source for base recalibrator
GMT GATK: add tmp dir option
InstData GATK: base recalibrator uses allocation tmp dir for gatk print reads
Merge remote-tracking branch upstream/$:{upbranch}