PALEOMIX v1.2.7

Added

• PALEOMIX now includes the 'Zonkey' pipeline, a pipeline for
  detecting equine F1 hybrids from archeological remains. Usage
  is described in the documentation.

Changed

• The wrongly named per-sample option 'Gender' in the phylogenetic
  pipeline makefile has been replaced with a 'Sex' option. This does not
  break backwards compatibility, and makefiles using the old name will still
  work correctly.
• The 'RescaleQualities' option has been merged with the 'mapDamage' Feature
  in the BAM pipeline makefile. The 'mapDamage' feature now takes the options
  'plot', 'model', and 'rescale', allowing more fine-grained control.

Fixed

• Fixed the phylogenetic pipeline complaining about missing sample genders
  (now sex) if no regions of interest had been specified. The pipeline will
  now complain about there being no regions of interest, instead.
• The 'random sampling' genotyper would misinterpret mapping qualities 10
  (encoded as '+') and 12 (encoded as '-') as indels, resulting in the
  genotyping failing. These mapping qualities are now correctly ignored.