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Revert "Bump to ADAM 0.23.0 release. (#4044)" #4428

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merged 1 commit into from Feb 26, 2018

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droazen
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@droazen droazen commented Feb 20, 2018

This reverts commit 8a366c7.

We noticed a major performance regression in BaseRecalibratorSpark and HaplotypeCallerSpark after we upgraded our ADAM dependency (see #4376). This PR reverts that upgrade for now until we understand the underlying cause.

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droazen commented Feb 20, 2018

@tomwhite Please review, and confirm that this resolves the performance issues you encountered.

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Codecov Report

Merging #4428 into master will increase coverage by 0.014%.
The diff coverage is 100%.

@@              Coverage Diff               @@
##             master     #4428       +/-   ##
==============================================
+ Coverage     79.04%   79.054%   +0.014%     
- Complexity    16447     16449        +2     
==============================================
  Files          1047      1047               
  Lines         59189     59190        +1     
  Branches       9672      9671        -1     
==============================================
+ Hits          46783     46792        +9     
+ Misses         8644      8639        -5     
+ Partials       3762      3759        -3
Impacted Files Coverage Δ Complexity Δ
...ngine/spark/datasources/ReferenceTwoBitSource.java 100% <100%> (+9.091%) 7 <3> (+1) ⬆️
...park/sv/discovery/alignment/AlignmentInterval.java 90.038% <0%> (+0.766%) 74% <0%> (+1%) ⬆️
...oadinstitute/hellbender/utils/gcs/BucketUtils.java 80% <0%> (+1.29%) 39% <0%> (ø) ⬇️
...e/hellbender/engine/spark/SparkContextFactory.java 73.973% <0%> (+2.74%) 11% <0%> (ø) ⬇️

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I ran the exome pipeline again with these changes and the performance regression went away.

@lbergelson lbergelson merged commit 9fe150c into master Feb 26, 2018
@lbergelson lbergelson deleted the dr_revert_adam_upgrade branch February 26, 2018 19:29
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4 participants