Proposal: deprecate FixBAMFile.java

[magicDGS]

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]

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]

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

[magicDGS]

Thanks @lbergelson and @yfarjoun!