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methylSig v0.4.3 (major bugfix)
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@rcavalcante rcavalcante released this 12 May 17:26
v0.4.3
089c561

Bug in methylSigReadData()

  • The problem: In #14, @bmreilly observed that adding more samples resulted in fewer sites tested for DM.
  • The reason: 060381b moved the minCount/maxCount filter from methylSigReadDataSingleFile() to methylSigReadData() after destranding. This way destranding would rescue +/- sites that individually were < minCount, but when destranded were > minCount. This fix introduced another bug whereby a site in any sample failing minCount/maxCount would remove this site from every sample. This behavior is consistent with the behavior in #14.
  • The fix: This release refactors methylSigReadData() and methylSigReadDataSingleFile() so that destranding and the minCount/maxCount filter are in methylSigReadDataSingleFile(), and only the site in the offending sample will be minCount/maxCount filtered. Included in the fix are new unit tests and new test files to fully ensure the behavior we expect.

Accessor for findOverlaps()

  • 9ba232c accesses queryHits with accessor function queryHits() instead of slots @ when filtering SNPs. Accessing with @ was causing Travis-CI build failures.
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