PALEOMIX v1.2.10

Added

• Preliminary support for CSI indexed BAM files, required for genomes with
  chromosomes > 2^29 - 1 bp in size. Support is still missing in HTSJDK, so
  GATK cannot currently be used with such genomes. CSI indexing is enabled
  automatically when required.

Fixed

• Reference sequences placed in the current directory no longer cause the
  BAM pipeline to complain about non-writable directories.
• The maximum number of temporary files used by picard will no longer be
  increased above the default value used by the picard tools.

Changed

• The 'Status' of processes terminated by the pipeline will now be reported
  as 'Automatically terminated by PALEOMIX'. This is to help differentiate
  between processes that failed or were killed by an external source, and
  processes that were cleaned up by the pipeline itself.
• Pretty-printing of commands shown when commands fail have been revised
  to make it more readable, including explicit descriptions when output
  is piped from one process to another and vice versa.
• Commands are now shown in a format more suitable for running on the
  command-line, instead of as a Python list, when a node fails. Pipes are
  still specified separately.
• Improved error messages for missing programs during version checks, and for
  exceptions raised when calling Popen during version checks.
• Strip MC tags from reads with unmapped mates during cleanup; this is
  required since Picard (v2.9.0) ValidateSamFile considers such tags invalid.