Skip to content

Release 0.7.0
Compare
Choose a tag to compare
@nh13 nh13 released this 06 Nov 20:43
0.7.0
5cff10d

Release 0.7.0 introduces the following changes to existing tools:

  • GroupReadsByUmi
    • check that the raw UMI tag is found foreach read (#406)
    • Fix log message in GroupReadsByUmi to be more accurate / less misleading (#436)
  • DemuxFastqs: enable --quality-encoding to be used on the command line (#417)
  • HapCutToVcf
    • fix ambiguous (IUPAC) reference bases on the fly #418)
    • add an option to skip indexing the output file (ex. when the input does not have CONTIG lines) #418)

In addition, the following new tools were added:

  • FindSwitchbackReads: Tool to detect templates with strand-switch events in them (#438)

The following API changes were also introduced:

  • FastqSource can handle read numbers > 2 (#408)
  • Fixed writing and parsing of Double.Nan, Double.PositiveInfinity and Double.NegativeInfinity in Metric classes (#411)
  • SamBuilder should accept missing bases and quals with a cigar (#424)
  • Add message to require() call in Sample (#425)
  • ReadStructure to allow and strip out whitespace within the read structure during parsing (#425)
  • ProgressLogger.record should return if logging was triggered and a method to log the last record (#421)
  • Bug fix: Metric.write was not closing its writer (#421)
  • Adding a few useful methods to Sequences (#421)
  • Metric now extends Commons Writer so we can use AsyncWriter on it (#437)
  • Improve the error message when validating a sample shee. (#412)
Assets 3
Loading