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Peak duplicate metrics; fix max fragment length measurement
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@umijh umijh released this 28 Jun 14:57
· 34 commits to master since this release
0.9.2
c8b6ee6

Correct maximum fragment length observation

  • The code didn't match its comment; when trying to ascertain the maximum proper fragment length, it was considering supplementary (chimeric) and secondary alignments. Corrected it to only measure the fragment size of primary alignments.

New metrics: duplicates in and out of peaks

  • Measure the fraction of duplicate reads outside of and within peaks.
  • Refactored some measurements, moving them from Metrics to Peaks.
  • Purged a bunch of YAGNI code.
  • Brought test coverage up to date.
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