• Extract CommandLineProgram finding/processing code for reuse. (#899)
• This makes CollectSequencingArtifactMetrics faster by reducing the number of HashMap.get() functions we call at every base of the traversal. (#912)
• Adding the option to not write out PG tags for MarkDuplicates and MergeBamAlignment. Default behavior is kept the same as it was before but you can get speed increases if you set them appropriately. (#907)