fixed bug

[davidbenjamin]

@LeeTL1220 This fixes the bug preventing Beri from updating to 4.0.8.0. I will put in an integration test but could you start looking at it now?

[davidbenjamin]

@LeeTL1220 I put in a test that fails without the patch.

[LeeTL1220]

Did you upload both the bai and bam? Otherwise, looks good feel free to merge.

[droazen]

@davidbenjamin Do we need to do another release for this?

[davidbenjamin]

@droazen Yes, please. Sorry for not catching this! Turns out that unpaired reads that pass all the M2 read filters and show evidence of a SNV are rare enough that they don't show up in any of the M2 validations.

[LeeTL1220]

@davidbenjamin @droazen Though the automated tests will now catch this (as of this PR).

[codecov-io]

Codecov Report

Merging #5121 into master will decrease coverage by <.001%.
The diff coverage is 85.714%.

@@               Coverage Diff               @@
##              master     #5121       +/-   ##
===============================================
- Coverage     86.507%   86.507%   -<.001%     
- Complexity     29260     29262        +2     
===============================================
  Files           1814      1814               
  Lines         135635    135641        +6     
  Branches       15063     15063               
===============================================
+ Hits          117334    117339        +5     
  Misses         12833     12833               
- Partials        5468      5469        +1

Impacted Files	Coverage Δ	Complexity Δ
...hellbender/tools/walkers/mutect/Mutect2Engine.java	90.968% <0%> (-0.645%)	59 <0> (ø)
...r/tools/walkers/mutect/Mutect2IntegrationTest.java	91.349% <100%> (+0.183%)	57 <1> (+1)	⬆️

[davidbenjamin]

@droazen thanks for merging. I wouldn't have had a chance until right now at this Toledo rest stop with Wifi.