BamUtil Version 1.0.10 released

[bamUtils]

BamUtil.1.0.10 Release Notes

• Requires, libStatGen version 1.0.10
• All
  • Add PhoneHome/version checking
  • Make sub-program names case independent
  • Fix Logger.cpp compiler warning
• Adds: explainFlags - describes the SAM/BAM flags based on the flag value
• Update to stats
  • Fix Stats to not try to not try to process a record after it is out of the loop (it would already have been processed or is invalid)
• Update to splitBam
  • fix description of --noeof option
• Update to writeRegion
  • add exclude/required flags
• Update to dedup & recab
  • Ignore secondary reads for dedup and making the recalibration table.
  • skip QC Failures
  • add excludeFlags parameters
• Update to clipOverlap
  • add exclude flags
  • fix bug for readName sorted when a read is filtered due to flags
  • add sorting validation
• Update to bam2FastQ
  • add --merge option to generate interleaved files.
  • update to open the input file before opening the output files, so if there is an error, the outputs aren't opened
• Update to mergeBam
• add option to ignore the RG PI field when checking headers
• add more informative header merge error messages

If you are interested in this Update, the new version can be downloaded at:

http://genome.sph.umich.edu/wiki/BamUtil#Releases

You must also update to the most recent version of libStatGen, 1.0.10, http://genome.sph.umich.edu/wiki/LibStatGen_Download

Let me know if you have any questions.

Mary Kate Wing