fulcrumgenomics / fgbio

Tools for working with genomic and high throughput sequencing data.
http://fulcrumgenomics.github.io/fgbio/
MIT License
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Make `PileupBuilder.includeMapPositionsOutsideFrInsert` intuitively correct #981

Closed clintval closed 4 months ago

clintval commented 4 months ago

Closes #980

clintval commented 4 months ago

@jrm5100 could I get your 👀 on this one?

Discussion in this thread: https://github.com/fulcrumgenomics/fgbio/issues/980

clintval commented 4 months ago

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:

codecov[bot] commented 4 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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

Additional details and impacted files ```diff @@ 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](https://app.codecov.io/gh/fulcrumgenomics/fgbio/pull/981/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=fulcrumgenomics) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/fulcrumgenomics/fgbio/pull/981/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=fulcrumgenomics) | `95.62% <100.00%> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=fulcrumgenomics#carryforward-flags-in-the-pull-request-comment) to find out more.

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