hammerlab / guacamole / 2593
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Files 88
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2593

Pull #617

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use main-class shorthand
Pull Request #617: upgrade hammerlab/spark-genomics deps

717 of 717 new or added lines in 57 files covered. (100.0%)

1869 of 2391 relevant lines covered (78.17%)

0.78 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
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 src/main/scala/org/hammerlab/guacamole/Main.scala
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 src/main/scala/org/hammerlab/guacamole/commands/SomaticStandardCaller.scala
1
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 src/main/scala/org/hammerlab/guacamole/filters/FishersExactTest.scala
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 src/main/scala/org/hammerlab/guacamole/filters/genotype/MinimumAlternateReadDepthFilter.scala
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 src/main/scala/org/hammerlab/guacamole/filters/genotype/MinimumLikelihoodFilter.scala
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 src/main/scala/org/hammerlab/guacamole/filters/genotype/ReadDepthFilter.scala
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 src/main/scala/org/hammerlab/guacamole/filters/somatic/SomaticMinimumLikelihoodFilter.scala
1
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 src/main/scala/org/hammerlab/guacamole/jointcaller/evidence/TumorDNASingleSampleSingleAlleleEvidence.scala
1
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 src/main/scala/org/hammerlab/guacamole/jointcaller/package.scala
1
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 src/main/scala/org/hammerlab/guacamole/jointcaller/pileup_summarization/ReadSubsequence.scala
1
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 src/main/scala/org/hammerlab/guacamole/pileup/Pileup.scala
1
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 src/main/scala/org/hammerlab/guacamole/readsets/rdd/PartitionedRegions.scala
1
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 src/main/scala/org/hammerlab/guacamole/reference/MapBackedReferenceSequence.scala
1
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 src/main/scala/org/hammerlab/guacamole/variants/Allele.scala
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 src/main/scala/org/hammerlab/guacamole/variants/GenotypeOutputArgs.scala
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 src/main/scala/org/hammerlab/guacamole/commands/SomaticJointCaller.scala
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 src/main/scala/org/hammerlab/guacamole/commands/VariantSupport.scala
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 src/main/scala/org/hammerlab/guacamole/reference/ArrayBackedReferenceSequence.scala
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 src/main/scala/org/hammerlab/guacamole/reference/ReferenceBroadcast.scala
3
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 src/main/scala/org/hammerlab/guacamole/filters/genotype/GenotypeFilter.scala
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 src/main/scala/org/hammerlab/guacamole/jointcaller/evidence/TumorRNASingleSampleSingleAlleleEvidence.scala
3
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 src/main/scala/org/hammerlab/guacamole/pileup/PileupElement.scala
4
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 src/main/scala/org/hammerlab/guacamole/commands/GermlineAssemblyCaller.scala
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 src/main/scala/org/hammerlab/guacamole/jointcaller/AlleleAtLocus.scala
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 src/main/scala/org/hammerlab/guacamole/jointcaller/pileup_summarization/PileupStats.scala
4
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 src/main/scala/org/hammerlab/guacamole/pileup/Alignment.scala
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 src/main/scala/org/hammerlab/guacamole/loci/partitioning/CappedRegionsPartitioner.scala
6
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 src/main/scala/org/hammerlab/guacamole/readsets/rdd/CoverageRDD.scala
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 src/main/scala/org/hammerlab/guacamole/loci/partitioning/LociPartitioning.scala
8
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 src/main/scala/org/hammerlab/guacamole/assembly/AssemblyUtils.scala
13
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 src/main/scala/org/hammerlab/guacamole/assembly/DeBruijnGraph.scala
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 src/main/scala/org/hammerlab/guacamole/commands/VAFHistogram.scala
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 src/main/scala/org/hammerlab/guacamole/jointcaller/VCFOutput.scala

Uncovered Existing Lines

Lines Coverage ∆ File
1
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 src/main/scala/org/hammerlab/guacamole/loci/partitioning/CappedRegionsPartitioner.scala
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 src/main/scala/org/hammerlab/guacamole/loci/partitioning/LociPartitioning.scala
1
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 src/main/scala/org/hammerlab/guacamole/commands/GermlineAssemblyCaller.scala
1
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 src/main/scala/org/hammerlab/guacamole/pileup/PileupElement.scala
1
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 src/main/scala/org/hammerlab/guacamole/jointcaller/evidence/TumorDNASingleSampleSingleAlleleEvidence.scala
1
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 src/main/scala/org/hammerlab/guacamole/assembly/DeBruijnGraph.scala
1
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 src/main/scala/org/hammerlab/guacamole/distributed/RegionsByContig.scala
2
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 src/main/scala/org/hammerlab/guacamole/jointcaller/InputCollection.scala
2
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 src/main/scala/org/hammerlab/guacamole/commands/VariantSupport.scala
2
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 src/main/scala/org/hammerlab/guacamole/jointcaller/evidence/MultiSampleMultiAlleleEvidence.scala
3
100.0
 src/main/scala/org/hammerlab/guacamole/commands/SomaticStandardCaller.scala
4
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 src/main/scala/org/hammerlab/guacamole/jointcaller/evidence/MultiSampleSingleAlleleEvidence.scala
5
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 src/main/scala/org/hammerlab/guacamole/reference/ReferenceBroadcast.scala
6
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 src/main/scala/org/hammerlab/guacamole/commands/SomaticJointCaller.scala
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 src/main/scala/org/hammerlab/guacamole/jointcaller/VCFOutput.scala
Jobs
ID Job ID Ran Files Coverage
1 2593.1 0
78.17
 Travis Job 2593.1
Source Files on build 2593
Detailed source file information is not available for this build.