Same as last commit for align_with_bwa_mem().
Same as last commit for align_with_bwa_mem().

woodymit/millstone,woodymit/millstone_accidental_source,churchlab/millstone,woodymit/millstone,woodymit/millstone_accidental_source,woodymit/millstone_accidental_source,woodymit/millstone_accidental_source,churchlab/millstone,woodymit/millstone,woodymit/millstone,churchlab/millstone,churchlab/millstone