PALEOMIX v1.2.5

Minor revision:

Changed

• Improved information capture when a node raises an unexpected exception,
  mainly for nodes implementing their own 'run' function (not CommandNodes).
• Improved printing of the state of output files when using the command-line
  option --list-output-files. Outdated files are now always listed as
  outdated, where previously these could be listed as 'Missing' if the task
  in question was queued to be run next.
• Don't attempt to validate prefixes when running 'trim_pipeline'; note that
  the structure of the Prefix section the makefile still has to be valid.
• Reverted commit normalizing the strand of unmapped reads.
• The commands 'paleomix coverage' and 'paleomix depths' now accept records
  lacking read-group information by default; these are record as in the
  sample and library columns. It is further possible to ignore all read-group
  information using the --ignore-readgroups command-line option.
• The 'bam_pipeline mkfile' command now does limited validation of input
  'SampleSheet.csv', prints generated targets sorted alphabetically, and
  automatically generates unique names for identically named lanes. Finally,
  the target template is not included automatically generating a makefile.
• The 'coverage' and 'depth' commands are now capable of processing files
  containing reads with and without read-groups, without requiring the use
  of the --ignore-readgroups command-line option. Furthermore, reads for
  which the read-group is missing in the BAM header are treated as if no
  readgroup was specified for that read.
• The 'coverage' and 'depth' command now checks that input BAM files are
  sorted during startup and while processing a file.
• Normalized information printed by different progress UIs (--progress-ui),
  and included the maximum number of threads allowed.
• Restructured CHANGELOG based on http://keepachangelog.com/

Fixed

• Fixed mislabeling of BWA nodes; all were labeled as 'SE'.
• Terminate read duplication checks when reaching the trailing, unmapped
  reads; this fixes uncontrolled memory growth when an alignment produces a
  large number of unmapped reads.
• Fixed the pipeline demanding the existence of files from lanes that had
  been entirely excluded due to ExcludeReads settings.
• Fixed some tasks needlessly depending on BAM files being indexed (e.g.
  depth histograms of a single BAM), resulting in missing file errors for
  certain makefile configurations.
• Fixed per-prefix scan for duplicate input data not being run if no BAMs
  were set to be generated in the makefile, i.e. if both 'RawBAM' and
  'RealignedBAM' was set to 'off'.

Deprecated

• Removed the BAM file from the bam_pipeline example, and added deprecation
  warning; support for including preexisting BAMs will be removed in a
  future version of PALEOMIX.