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

Add DownsampleVcf tool #974

Open TedBrookings opened 5 months ago

TedBrookings commented 5 months ago

Adds a tool to downsample VCFs based on allele depths. Currently only handles biallelic variants.

codecov[bot] commented 5 months ago

Codecov Report

Attention: Patch coverage is 95.69892% with 4 lines in your changes are missing coverage. Please review.

Project coverage is 95.64%. Comparing base (3a74fd2) to head (9a2d510).

:exclamation: Current head 9a2d510 differs from pull request most recent head 75de344. Consider uploading reports for the commit 75de344 to get more accurate results

Files Patch % Lines
.../scala/com/fulcrumgenomics/vcf/DownsampleVcf.scala 95.69% 4 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #974 +/- ## ========================================== + Coverage 95.62% 95.64% +0.01% ========================================== Files 126 127 +1 Lines 7364 7457 +93 Branches 506 521 +15 ========================================== + Hits 7042 7132 +90 - Misses 322 325 +3 ``` | [Flag](https://app.codecov.io/gh/fulcrumgenomics/fgbio/pull/974/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/974/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=fulcrumgenomics) | `95.64% <95.69%> (+0.01%)` | :arrow_up: | 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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