Pulled the HaplotypeCallerIntegration tests into a common interface between spark and non-spark #5451
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tomwhite
approved these changes
Dec 10, 2018
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@jamesemery it would be good to get this one in (needs rebasing). |
…en spark and non-spark versions
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@tomwhite This should be good for you to take a look |
tomwhite
approved these changes
Feb 26, 2019
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| import java.io.File; | |||
| import java.util.Collections; | |||
| import java.util.List; | |||
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| import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerIntegrationTest; | |||
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| @Test(groups = {"variantcalling"}) | |||
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Should also be in the spark group.
| vc.getAlternateAllele(0).equals(Allele.NON_REF_ALLELE); | ||
| @Override | ||
| public List<String> getToolSpecificArguments() { | ||
| return Collections.emptyList(); |
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Maybe make this the default implementation (i.e. in the abstract class) and just have the Spark version override it.
Codecov Report
@@ Coverage Diff @@
## master #5451 +/- ##
===============================================
- Coverage 87.069% 80.155% -6.914%
+ Complexity 31875 30203 -1672
===============================================
Files 1940 1941 +1
Lines 146738 146745 +7
Branches 16226 16226
===============================================
- Hits 127764 117624 -10140
- Misses 13061 23431 +10370
+ Partials 5913 5690 -223
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@jamesemery This depended on #5416, which has since been merged. What's the status of this PR now? |
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This was a quick job, I think more than anything it highlighted that we are missing many features in spark as of right now.
Depends On #5416