hammerlab / guacamole / 2590
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2590

Pull #617

travis-ci

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use forked ADAM PhredUtils
Pull Request #617: upgrade hammerlab/spark-genomics deps

719 of 719 new or added lines in 57 files covered. (100.0%)

1859 of 2402 relevant lines covered (77.39%)

0.77 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
1
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 src/main/scala/org/hammerlab/guacamole/Main.scala
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 src/main/scala/org/hammerlab/guacamole/filters/FishersExactTest.scala
1
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 src/main/scala/org/hammerlab/guacamole/filters/genotype/MinimumAlternateReadDepthFilter.scala
1
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 src/main/scala/org/hammerlab/guacamole/filters/genotype/MinimumLikelihoodFilter.scala
1
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 src/main/scala/org/hammerlab/guacamole/filters/genotype/ReadDepthFilter.scala
1
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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
1
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 src/main/scala/org/hammerlab/guacamole/variants/GenotypeOutputArgs.scala
2
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 src/main/scala/org/hammerlab/guacamole/commands/SomaticJointCaller.scala
2
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 src/main/scala/org/hammerlab/guacamole/commands/SomaticStandardCaller.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/reference/ArrayBackedReferenceSequence.scala
2
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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
3
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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
4
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 src/main/scala/org/hammerlab/guacamole/jointcaller/AlleleAtLocus.scala
4
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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
6
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 src/main/scala/org/hammerlab/guacamole/readsets/rdd/CoverageRDD.scala
7
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 src/main/scala/org/hammerlab/guacamole/loci/partitioning/CappedRegionsPartitioner.scala
7
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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
12
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 src/main/scala/org/hammerlab/guacamole/assembly/DeBruijnGraph.scala
13
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 src/main/scala/org/hammerlab/guacamole/commands/VAFHistogram.scala
23
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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/distributed/SingleContigRegionIterator.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/distributed/RegionsByContig.scala
1
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 src/main/scala/org/hammerlab/guacamole/jointcaller/evidence/TumorDNASingleSampleSingleAlleleEvidence.scala
1
100.0
 src/main/scala/org/hammerlab/guacamole/assembly/DeBruijnGraph.scala
1
100.0
 src/main/scala/org/hammerlab/guacamole/filters/somatic/SomaticAverageMappingQualityFilter.scala
1
100.0
 src/main/scala/org/hammerlab/guacamole/pileup/PileupElement.scala
1
100.0
 src/main/scala/org/hammerlab/guacamole/loci/partitioning/MicroRegionPartitioner.scala
1
100.0
 src/main/scala/org/hammerlab/guacamole/commands/VAFHistogram.scala
1
100.0
 src/main/scala/org/hammerlab/guacamole/loci/partitioning/LociPartitioning.scala
1
100.0
 src/main/scala/org/hammerlab/guacamole/windowing/SlidingWindow.scala
1
100.0
 src/main/scala/org/hammerlab/guacamole/loci/partitioning/CappedRegionsPartitioner.scala
2
100.0
 src/main/scala/org/hammerlab/guacamole/jointcaller/evidence/MultiSampleMultiAlleleEvidence.scala
2
100.0
 src/main/scala/org/hammerlab/guacamole/commands/VariantSupport.scala
2
100.0
 src/main/scala/org/hammerlab/guacamole/jointcaller/InputCollection.scala
6
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 src/main/scala/org/hammerlab/guacamole/jointcaller/evidence/MultiSampleSingleAlleleEvidence.scala
6
100.0
 src/main/scala/org/hammerlab/guacamole/reference/ReferenceBroadcast.scala
7
100.0
 src/main/scala/org/hammerlab/guacamole/commands/SomaticJointCaller.scala
7
100.0
 src/main/scala/org/hammerlab/guacamole/commands/SomaticStandardCaller.scala
9
100.0
 src/main/scala/org/hammerlab/guacamole/jointcaller/VCFOutput.scala
Jobs
ID Job ID Ran Files Coverage
1 2590.1 0
77.39
 Travis Job 2590.1
Source Files on build 2590
Detailed source file information is not available for this build.