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Make PileupBuilder.includeMapPositionsOutsideFrInsert intuitively correct #981

Merged
merged 4 commits into from
Apr 25, 2024
Merged

Make PileupBuilder.includeMapPositionsOutsideFrInsert intuitively correct #981

merged 4 commits into from
Apr 25, 2024

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clintval
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Closes #980

@clintval clintval requested a review from tfenne April 24, 2024 01:21
@clintval clintval mentioned this pull request Apr 24, 2024
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clintval commented Apr 24, 2024 •
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@jrm5100 could I get your 👀 on this one?

Discussion in this thread: #980

@clintval clintval assigned clintval and unassigned tfenne Apr 24, 2024
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jrm5100 reviewed Apr 24, 2024
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See discussion here: #980 (comment)

src/test/scala/com/fulcrumgenomics/bam/pileup/PileupBuilderTest.scala Outdated Show resolved Hide resolved
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We've settled on how the filter is supposed to work and I've updated the documentation.

The filter should now be more obvious in how it is supposed to be used.

No functional change will occur when this PR is merged. The only updates:

  • A variable name was updated to be logically correct
  • An additional unit test was added for sanity sake
  • Better documentation exists for the filter's intended use case

jrm5100
jrm5100 reviewed Apr 25, 2024
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This looks solid. The one test just needs updating (though I may have the intention of it wrong).

src/test/scala/com/fulcrumgenomics/bam/pileup/PileupBuilderTest.scala Show resolved Hide resolved
src/test/scala/com/fulcrumgenomics/bam/pileup/PileupBuilderTest.scala Outdated Show resolved Hide resolved
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codecov bot commented Apr 25, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.62%. Comparing base (3a74fd2) to head (c02e0b3).

Additional details and impacted files 
@@           Coverage Diff           @@
##             main     #981   +/-   ##
=======================================
  Coverage   95.62%   95.62%           
=======================================
  Files         126      126           
  Lines        7364     7364           
  Branches      506      500    -6     
=======================================
  Hits         7042     7042           
  Misses        322      322
Flag Coverage Δ
unittests 95.62% <100.00%> (ø)

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@clintval clintval merged commit a82cfe0 into main Apr 25, 2024
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@clintval clintval deleted the cv_fixup_fr_filter branch April 25, 2024 23:30
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@nh13 nh13 nh13 approved these changes

@tfenne tfenne Awaiting requested review from tfenne tfenne is a code owner

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bug: the logic for the PileupBuilder includeMapPositionsOutsideFrInsert filter is wrong
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