PALEOMIX v1.2.8

This is minor release of PALEOMIX, which includes an important bug-fix to BAM Pipelines using the BWA
'mem' or 'bwasw' algorithms. Previously, user-specified command-line parameters would not be correctly
applied to the BWA commands, when either of these two algorithms were used. This has now been
corrected.

Added

• Added FILTER entry for 'F' filter used in vcf_filter. This corresponds to
  heterozygous sites where the allele frequency was not determined.
• Added 'dupcheck' command. This command roughly corresponds to the
  DetectInputDuplication step that is part of the BAM pipeline, and attempts
  to identify duplicate data (not PCR duplicates), by locating reads mapped
  to the same position, with the same name, sequence, and quality scores.
• Added link to sample data used in publication to the Zonkey documentation.

Changed

• Only letters, numbers, and '-', '_', and '.' are allowed in sample-names
  used in Zonkey, in order to prevent invalid filenames and certain programs
  breaking on whitespace. Trailing whitespace is stripped.
• Show more verbose output when building Zonkey pipelines.
• Picard tools version 1.137 or later is now required by the BAM pipeline.
  This is nessesary as newer BAM files (header version 1.5) would fail to
  validate when using earlier versions of Picard tools.

Fixed

• Fixed validation nodes failing on output paths without a directory.
• Fixed possible uncaught exceptions when terminating cat commands used by
  FASTQ validation nodes resulting in loss of error messages.
• Fixed makefile validation failing with an unhandled TypeError if unhashable
  types were found in unexpected locations. For example, a dict found where a
  subset of strings were allowed. These now result in a proper MakeFileError.
• Fixed user options in the 'BWA' section of the BAM Pipeline makefiles not
  being correctly applied when using the 'mem' or the 'bwasw' algorithms.
• Fixed some unit tests failing when the environment caused getlogin to fail.