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enable -L to read Feature Files from Paths #4854

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merged 1 commit into from
Jun 7, 2018
Merged

enable -L to read Feature Files from Paths #4854

merged 1 commit into from
Jun 7, 2018

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lbergelson
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@lbergelson
enable -L to read Feature Files from Paths
f6a9fa5 
* expand -L support for Feature Files to work with Paths
* previously interval files could be read from Paths, but not feature
files like vcf and bed
* fixes #4852
@lbergelson
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@droazen @SHuang-Broad This should fix the problem we were talking about. Could someone review it?

@droazen droazen self-assigned this Jun 7, 2018
SHuang-Broad
SHuang-Broad approved these changes Jun 7, 2018
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👍
Also testing working on a real Spark cluster.

droazen
droazen approved these changes Jun 7, 2018
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👍 looks good to me -- merge once tests pass

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Codecov Report

Merging #4854 into master will decrease coverage by 0.084%.
The diff coverage is 100%.

@@              Coverage Diff               @@
##             master     #4854       +/-   ##
==============================================
- Coverage     80.35%   80.265%   -0.084%     
  Complexity    17712     17712               
==============================================
  Files          1088      1088               
  Lines         63974     64040       +66     
  Branches      10313     10333       +20     
==============================================
- Hits          51403     51402        -1     
- Misses         8558      8625       +67     
  Partials       4013      4013
Impacted Files Coverage Δ Complexity Δ
...oadinstitute/hellbender/engine/FeatureManager.java 86.275% <100%> (ø) 47 <3> (ø) ⬇️
...broadinstitute/hellbender/utils/IntervalUtils.java 91.516% <100%> (-0.015%) 181 <0> (ø)
...hellbender/tools/walkers/mutect/Mutect2Engine.java 60.891% <0%> (-30.22%) 50% <0%> (ø)

@lbergelson lbergelson merged commit f4225b8 into master Jun 7, 2018
@lbergelson lbergelson deleted the lb_enable_paths_for_intervals branch June 7, 2018 18:21
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@SHuang-Broad SHuang-Broad SHuang-Broad approved these changes

@droazen droazen droazen approved these changes

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Successfully merging this pull request may close these issues.

Cannot read BED file stored in HDFS as interval list file
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@lbergelson @codecov-io @droazen @SHuang-Broad