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breseq v0.34.0

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@jeffreybarrick jeffreybarrick released this 14 Sep 02:55
· 243 commits to master since this release
  • Fixed bug where two rejected JC evidence items could predict a mutation.
  • Added new option --junction-minimum-pr-no-read-start-per-position to prevent saturation
    of coverage in high-coverage samples from leading to rejection of valid JC prediction.
    Set this option to 0.0 if you want to use the behavior of previous versions.
  • Changed default for --consensus-frequency-cutoff to be 0.8 in polymorphism mode,
    instead of 0.0, to prevent accepting rejected polymorphism RA items as consensus predictions.
  • Added the ability to predict DEL spanning the origin of a circular reference sequence.
  • Changed plotting scripts to be more compatible with fonts available to different versions of R.
  • Miscellaneous fixes to make gdtools commands more robust.