hammerlab / guacamole / 2595
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Files 91
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2595

Pull #617

travis-ci

web-flow 
upgrade plugin, input/samples, readsets args
Pull Request #617: upgrade hammerlab/spark-genomics deps

835 of 835 new or added lines in 62 files covered. (100.0%)

1890 of 2421 relevant lines covered (78.07%)

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/SomaticJointCaller.scala
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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
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 src/main/scala/org/hammerlab/guacamole/jointcaller/Inputs.scala
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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
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 src/main/scala/org/hammerlab/guacamole/jointcaller/pileup_summarization/ReadSubsequence.scala
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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
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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/VariantSupport.scala
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 src/main/scala/org/hammerlab/guacamole/jointcaller/Samples.scala
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 src/main/scala/org/hammerlab/guacamole/jointcaller/evidence/MultiSampleSingleAlleleEvidence.scala
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 src/main/scala/org/hammerlab/guacamole/reference/ArrayBackedReferenceSequence.scala
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 src/main/scala/org/hammerlab/guacamole/commands/SomaticStandardCaller.scala
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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/Sample.scala
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 src/main/scala/org/hammerlab/guacamole/jointcaller/evidence/TumorRNASingleSampleSingleAlleleEvidence.scala
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 src/main/scala/org/hammerlab/guacamole/pileup/PileupElement.scala
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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
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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
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
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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/jointcaller/VCFOutput.scala
1
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 src/main/scala/org/hammerlab/guacamole/commands/SomaticJointCaller.scala
1
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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/distributed/RegionsByContig.scala
1
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 src/main/scala/org/hammerlab/guacamole/loci/partitioning/MicroRegionPartitioner.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/assembly/DeBruijnGraph.scala
2
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 src/main/scala/org/hammerlab/guacamole/jointcaller/evidence/MultiSampleSingleAlleleEvidence.scala
2
100.0
 src/main/scala/org/hammerlab/guacamole/commands/VariantSupport.scala
2
100.0
 src/main/scala/org/hammerlab/guacamole/reference/ReferenceBroadcast.scala
Jobs
ID Job ID Ran Files Coverage
1 2595.1 0
78.07
 Travis Job 2595.1
Source Files on build 2595
Detailed source file information is not available for this build.