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add elapsed time to assembly info in intervals file #3629

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merged 1 commit into from Sep 28, 2017

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tedsharpe
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Here's a tiny commit that's mostly just code cleanup. @SHuang-Broad -- I sprinkled some "final"s around.

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Nice! 👍

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codecov-io commented Sep 27, 2017

Codecov Report

Merging #3629 into master will increase coverage by 0.01%.
The diff coverage is 92.857%.

@@              Coverage Diff               @@
##              master     #3629      +/-   ##
==============================================
+ Coverage     79.774%   79.784%   +0.01%     
- Complexity     18235     18238       +3     
==============================================
  Files           1225      1225              
  Lines          66978     66983       +5     
  Branches       10449     10449              
==============================================
+ Hits           53431     53442      +11     
+ Misses          9324      9318       -6     
  Partials        4223      4223
Impacted Files Coverage Δ Complexity Δ
...ellbender/tools/spark/sv/evidence/KmerCounter.java 100% <ø> (ø) 6 <0> (ø) ⬇️
...spark/sv/evidence/FindBreakpointEvidenceSpark.java 67.317% <100%> (+0.89%) 50 <0> (ø) ⬇️
...ols/spark/sv/evidence/AlignedAssemblyOrExcuse.java 90.909% <100%> (+0.284%) 43 <1> (+1) ⬆️
...r/tools/spark/sv/evidence/QNameIntervalFinder.java 100% <100%> (ø) 6 <1> (ø) ⬇️
...adinstitute/hellbender/utils/spark/SparkUtils.java 74.138% <66.667%> (-0.862%) 11 <2> (+2)
...er/tools/spark/sv/discovery/AlignmentInterval.java 88.889% <0%> (ø) 52% <0%> (ø) ⬇️
...e/hellbender/engine/spark/SparkContextFactory.java 73.973% <0%> (+2.74%) 11% <0%> (ø) ⬇️

import org.apache.log4j.Logger;
import org.apache.spark.broadcast.Broadcast;

public class SparkUtils {
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There's already a SparkUtils.java living in org.broadinstitute.hellbender.utils.spark. Maybe this can be moved there...

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Thanks. Moved it there, as you suggested.

@tedsharpe tedsharpe force-pushed the tws_add_elapsed_time_to_intervals_file branch from fba6f1c to 6c62ea9 Compare September 28, 2017 15:40
@tedsharpe tedsharpe force-pushed the tws_add_elapsed_time_to_intervals_file branch from 6c62ea9 to 1e5a4f3 Compare September 28, 2017 18:15
@tedsharpe tedsharpe merged commit 72cdd48 into master Sep 28, 2017
@tedsharpe tedsharpe deleted the tws_add_elapsed_time_to_intervals_file branch September 28, 2017 19:09
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4 participants