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  1. Data Management
  2. DM-11628

Fix minor bugs in peak culling

    Details

    • Type: Bug
    • Status: Done
    • Resolution: Done
    • Fix Version/s: None
    • Component/s: pipe_tasks
    • Labels:
      None
    • Templates:
    • Story Points:
      1
    • Sprint:
      DRP F17-3
    • Team:
      Data Release Production

      Description

      Sogo Mineo reports another bug in peak culling that makes it hard to disable via configuration:

      The docstring of class CullPeaksConfig says:

      To disable peak culling, simply set nBandsSafe=1.

      If I assume `nBandsSafe` is a typo for `nBandsSufficient`
      and set nBandsSufficient = 1,
      then the condition for a peak to be kept:

      if ((rank < self.config.cullPeaks.rankSufficient) or
      (self.config.cullPeaks.nBandsSufficient > 1 and
      sum([peak.get(k) for k in keys]) >= self.config.cullPeaks.nBandsSufficient) or
      (rank < self.config.cullPeaks.rankConsidered and
      rank < self.config.cullPeaks.rankNormalizedConsidered * familySize)):

      will be equivalent to:

      if ((rank < self.config.cullPeaks.rankSufficient) or
      (rank < self.config.cullPeaks.rankConsidered and
      rank < self.config.cullPeaks.rankNormalizedConsidered * familySize)):

      and peak culling will be still active in spite of the instruction of the docstring.

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              • Assignee:
                jbosch Jim Bosch
                Reporter:
                jbosch Jim Bosch
                Reviewers:
                Paul Price
                Watchers:
                Jim Bosch, Paul Price
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                • Created:
                  Updated:
                  Resolved:

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