PALEOMIX v1.3.4

Added

• Added support for the --collapse-conservatively AdapterRemoval option.

Changed

• Avoid creating log files on invalid commandline arguments.
• The directory for the log-file is created automatically if it does not exist.
• No longer prints stack-trace if the user terminates a pipeline wiht Ctrl + C.
• Log-level command-line options are now case insensitive.
• The default number of threads used by AdapterRemova, Bowtie2, and BWA are now scaled
  based on the available number of cores instead of defaulting to 1 thread.
• Less exhaustive validation of .bai index files using picard ValidateSamFile. The
  overhead of validating these files was excessive in light of the small benefit.

Fixed

• Fixed regression causing certain option to not be applied when mapping with BWA.
• Fixed --log-level not having an effect.
• Fixed possible infinite recursion when using lazily created log-files.
• Fixed BAM pipeline failing if mapDamage feature was not explicitly set.
• Fixed default values of 0 or 1 not being listed in commnad-line help text.