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Proposal: deprecate FixBAMFile.java #947

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merged 1 commit into from Aug 18, 2017

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@magicDGS
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commented Jul 27, 2017

Description

The FixBAMFile is an undocumented and untested feature that does not add anything to the HTSJDK as a library. I propose to deprecate this class and remove it eventually.

Checklist

  • Code compiles correctly
  • New tests covering changes and new functionality
  • All tests passing
  • Extended the README / documentation, if necessary
  • Is not backward compatible (breaks binary or source compatibility)
@codecov-io

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commented Jul 27, 2017

Codecov Report

Merging #947 into master will increase coverage by 0.009%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master      #947       +/-   ##
===============================================
+ Coverage     65.466%   65.475%   +0.009%     
- Complexity      7342      7343        +1     
===============================================
  Files            528       528               
  Lines          31980     31980               
  Branches        5467      5467               
===============================================
+ Hits           20936     20939        +3     
+ Misses          8891      8889        -2     
+ Partials        2153      2152        -1
Impacted Files Coverage Δ Complexity Δ
src/main/java/htsjdk/samtools/FixBAMFile.java 0% <ø> (ø) 0 <0> (ø) ⬇️
...sjdk/samtools/util/Md5CalculatingOutputStream.java 76.923% <0%> (+7.692%) 9% <0%> (+1%) ⬆️
@lbergelson

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commented Aug 18, 2017

@magicDGS I had no idea this thing was in htsjdk. 👍

@lbergelson lbergelson merged commit dcff7f5 into samtools:master Aug 18, 2017

4 checks passed

codecov/changes No unexpected coverage changes found.
Details
codecov/patch Coverage not affected when comparing 1969eb8...cafc555
Details
codecov/project 65.475% (+0.009%) compared to 1969eb8
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continuous-integration/travis-ci/pr The Travis CI build passed
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@magicDGS magicDGS deleted the bioinformagik:dgs_deprecate_FixBAMFile branch Aug 21, 2017

@magicDGS

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commented Aug 21, 2017

Thanks @lbergelson and @yfarjoun!

@magicDGS magicDGS restored the bioinformagik:dgs_deprecate_FixBAMFile branch Jun 28, 2018

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