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fulcrumgenomics / fgbio

Tools for working with genomic and high throughput sequencing data.
http://fulcrumgenomics.github.io/fgbio/
MIT License
309 stars 67 forks source link

Validate IO in SortBam to provide nicer exceptions #994

Closed nh13 closed 1 month ago

nh13 commented 3 months ago

Using the Io.assert* within the constructor will yield better error messages for the user.

Also added an explicit close to the input SamSource

codecov[bot] commented 3 months ago

Codecov Report

Attention: Patch coverage is 0% with 3 lines in your changes are missing coverage. Please review.

Project coverage is 95.61%. Comparing base (d5b38ca) to head (adb0693).

Files Patch % Lines
...c/main/scala/com/fulcrumgenomics/bam/SortBam.scala 0.00% 3 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #994 +/- ## ========================================== - Coverage 95.62% 95.61% -0.02% ========================================== Files 126 126 Lines 7364 7365 +1 Branches 500 510 +10 ========================================== Hits 7042 7042 - Misses 322 323 +1 ``` | [Flag](https://app.codecov.io/gh/fulcrumgenomics/fgbio/pull/994/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/994/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=fulcrumgenomics) | `95.61% <0.00%> (-0.02%)` | :arrow_down: | 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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