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Use bgzip as default for writing .gz files #253

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merged 6 commits into from
Dec 27, 2021
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@alumi alumi commented Dec 24, 2021

Fixes #251

This PR changes the behavior of cljam.util/compressor-output-stream.
It now returns BGZFOutputStream instead of GzipCompressorOutputStream for files with .gz extension.
Since BGZIP is just a special case of GZIP, existing codes using cljam.util/compressor-output-stream with .gz should still work.
To get GzipCompressorOutputStream, we can use the 2nd argument or .gzip extension.

This PR also includes

  • Update log4j to 2.17.0
  • Some minor fixes suggested by linters

@alumi alumi requested review from niyarin and r6eve December 24, 2021 04:50
@alumi alumi requested a review from a team as a code owner December 24, 2021 04:50
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codecov bot commented Dec 24, 2021

Codecov Report

Merging #253 (ebac5b4) into master (7e7ba7f) will decrease coverage by 0.10%.
The diff coverage is 53.84%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #253      +/-   ##
==========================================
- Coverage   88.70%   88.60%   -0.11%     
==========================================
  Files          76       76              
  Lines        6305     6308       +3     
  Branches      438      441       +3     
==========================================
- Hits         5593     5589       -4     
- Misses        274      278       +4     
- Partials      438      441       +3     
Impacted Files Coverage Δ
src/cljam/util.clj 80.95% <53.84%> (-10.58%) ⬇️
src/cljam/algo/sorter.clj 92.15% <0.00%> (-0.08%) ⬇️

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@alumi alumi removed the request for review from a team December 24, 2021 05:08
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@r6eve r6eve left a comment

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LGTM

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@niyarin niyarin left a comment

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LGTM 👍

@niyarin niyarin merged commit 9990510 into master Dec 27, 2021
@niyarin niyarin deleted the feature/bgzip-vcf-writer branch December 27, 2021 00:54
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alumi commented Dec 27, 2021

@r6eve @niyarin Thank you for reviewing! 👍

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Successfully merging this pull request may close these issues.

Bgziped VCF is illegal.
3 participants