Go back to using old bwa align for now.
Go back to using old bwa align for now.

See #93.

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