broadinstitute / hellbender / 2687
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LAST BUILD BRANCH: dr_disentangle_spark_and_dataflow
DEFAULT BRANCH: master
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Files 524
Run time 15s
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travis-ci

akiezun 
count reads in spark + integration test

21 of 21 new or added lines in 2 files covered. (100.0%)

5140 of 27342 relevant lines covered (18.8%)

0.19 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
18
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountReadsSpark.java

Uncovered Existing Lines

Lines Coverage ∆ File
1
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 src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/DbsnpArgumentCollection.java
1
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 src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/OptionalVariantInputArgumentCollection.java
1
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 src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineProgramGroup.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReferenceShard.java
1
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/VariantShard.java
1
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 src/main/java/org/broadinstitute/hellbender/engine/filters/VariantFilterLibrary.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSpark.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/JoinReadsWithVariants.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/SparkCommandLineProgram.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/BaseDistributionByCycleMetrics.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/JumpingLibraryMetrics.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/RnaSeqMetrics.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/RrbsCpgDetailMetrics.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/RrbsSummaryMetrics.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/InsertSizeMetrics.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordanceDetailMetrics.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/readersplitters/ReaderSplitter.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/interfaces/GenotypeAnnotation.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/collections/NestedIntegerArray.java
1
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 src/main/java/org/broadinstitute/hellbender/utils/gene/GeneAnnotationReader.java
1
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 src/main/java/org/broadinstitute/hellbender/utils/help/HelpConstants.java
1
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 src/main/java/org/broadinstitute/hellbender/utils/read/GATKRead.java
1
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 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportColumn.java
2
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 src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/OptionalIntervalArgumentCollection.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/coders/VariantCoder.java
2
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/transforms/KeyReadsByRefShard.java
2
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/transforms/PairReadWithRefBases.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/engine/filters/ReadNameReadFilter.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/metrics/SAMRecordAndReferenceMultiLevelCollector.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/metrics/SAMRecordMultiLevelCollector.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/CountReadsDataflow.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/PrintReadsDataflow.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorTransform.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/RecalibrationTablesMerger.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/CountReadsDataflowTransform.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/AlignmentSummaryMetrics.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/readersplitters/LibraryNameSplitter.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/readersplitters/ReadGroupIdSplitter.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/readersplitters/SampleNameSplitter.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/gene/LocusFunction.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/read/GATKReadToBDGAlignmentRecordConverter.java
2
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 src/main/java/org/broadinstitute/hellbender/utils/recalibration/EventType.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/R/RScriptExecutorException.java
2
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 src/main/java/org/broadinstitute/hellbender/utils/runtime/StreamLocation.java
2
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 src/main/java/org/broadinstitute/hellbender/utils/text/XReadLines.java
2
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 src/main/java/org/broadinstitute/hellbender/utils/variant/DbSnpVariantType.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java
3
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 src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/OpticalDuplicatesArgumentCollection.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/DataFlowProgramGroup.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/ExomeAnalysisProgramGroup.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/IntervalProgramGroup.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/MiscProgramGroup.java
3
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 src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/QCProgramGroup.java
3
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 src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/ReadProgramGroup.java
3
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 src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/SparkProgramGroup.java
3
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 src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/VariantProgramGroup.java
3
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/transforms/GetOverlappingReadsAndVariants.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/engine/filters/MappingQualityReadFilter.java
3
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 src/main/java/org/broadinstitute/hellbender/engine/filters/ReadFilter.java
3
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 src/main/java/org/broadinstitute/hellbender/engine/filters/ReadLengthReadFilter.java
3
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 src/main/java/org/broadinstitute/hellbender/engine/filters/ReadStrandFilter.java
3
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 src/main/java/org/broadinstitute/hellbender/metrics/MultiLevelMetrics.java
3
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 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/CountBasesDataflow.java
3
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 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/FlagStatDataflow.java
3
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 src/main/java/org/broadinstitute/hellbender/tools/readersplitters/ReadGroupSplitter.java
3
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantDatum.java
3
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 src/main/java/org/broadinstitute/hellbender/transformers/ReadTransformer.java
3
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 src/main/java/org/broadinstitute/hellbender/utils/NGSPlatform.java
3
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 src/main/java/org/broadinstitute/hellbender/utils/reference/ReferenceBases.java
3
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 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportDataType.java
3
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 src/main/java/org/broadinstitute/hellbender/utils/runtime/StreamOutput.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/RequiredReferenceInputArgumentCollection.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/transforms/composite/AddContextDataToRead.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/engine/filters/ReadGroupReadFilter.java
4
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 src/main/java/org/broadinstitute/hellbender/engine/ReferenceDataSource.java
4
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 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorFn.java
4
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 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/PrintReadsDataflowTransform.java
4
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/MergeCommonSuffices.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java
4
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibratorArgumentCollection.java
4
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 src/main/java/org/broadinstitute/hellbender/utils/LoggingUtils.java
4
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 src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/ReadEndsForMarkDuplicates.java
4
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 src/main/java/org/broadinstitute/hellbender/utils/read/ReadsWriteFormat.java
4
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 src/main/java/org/broadinstitute/hellbender/utils/samples/Sex.java
4
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 src/main/java/org/broadinstitute/hellbender/utils/UnsignedTypeUtil.java
5
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 src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/RequiredIntervalArgumentCollection.java
5
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 src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/RequiredReadInputArgumentCollection.java
5
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 src/main/java/org/broadinstitute/hellbender/cmdline/StrictBooleanConverter.java
5
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReferenceDataflowSource.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/PTransformSAM.java
5
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 src/main/java/org/broadinstitute/hellbender/engine/filters/FragmentLengthReadFilter.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/JsonSerializer.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/tools/CountBases.java
5
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 src/main/java/org/broadinstitute/hellbender/tools/CountReads.java
5
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/filter/DepthFilter.java
5
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/filter/GenotypeQualityFilter.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTest.java
5
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ClippingRankSumTest.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityRankSumTest.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/CountVariants.java
5
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 src/main/java/org/broadinstitute/hellbender/utils/reference/ReferenceUtils.java
5
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 src/main/java/org/broadinstitute/hellbender/utils/text/parsers/TabbedInputParser.java
6
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 src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/OptionalReadInputArgumentCollection.java
6
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/DataflowCommandLineProgram.java
6
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReferenceHadoopSource.java
6
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/RefWindowFunctions.java
6
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/transforms/examples/TransformExample.java
6
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 src/main/java/org/broadinstitute/hellbender/engine/filters/LibraryReadFilter.java
6
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 src/main/java/org/broadinstitute/hellbender/engine/filters/SampleReadFilter.java
6
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 src/main/java/org/broadinstitute/hellbender/metrics/SAMRecordAndReference.java
6
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6
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6
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/SplitCommonSuffices.java
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 src/main/java/org/broadinstitute/hellbender/tools/PrintReads.java
9
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9
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 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/FlagStatusDataflowTransform.java
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 src/main/java/org/broadinstitute/hellbender/tools/exome/TargetCollections.java
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/AddCommentsToBam.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/CompareSAMs.java
12
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ChromosomeCounts.java
12
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 src/main/java/org/broadinstitute/hellbender/utils/collections/IntervalsSkipListOneContig.java
12
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 src/main/java/org/broadinstitute/hellbender/utils/genotyper/IndexedSampleList.java
12
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 src/main/java/org/broadinstitute/hellbender/utils/test/ArgumentsBuilder.java
13
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/RefAPISource.java
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 src/main/java/org/broadinstitute/hellbender/engine/IntervalWalker.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/GatherBamFiles.java
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13
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/MergeTails.java
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 src/main/java/org/broadinstitute/hellbender/utils/samples/Sample.java
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 src/main/java/htsjdk/samtools/reference/HadoopFastaSequenceIndexEntry.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/SamFormatConverter.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/ByIntervalListVariantContextIterator.java
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/SeqVertex.java
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 src/main/java/org/broadinstitute/hellbender/utils/genotyper/IndexedAlleleList.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordanceContingencyMetrics.java
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/SampleList.java
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/TandemRepeat.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/Transition.java
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 src/main/java/org/broadinstitute/hellbender/utils/codecs/table/TableFeature.java
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 src/main/java/org/broadinstitute/hellbender/utils/illumina/IlluminaAdapterPair.java
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 src/main/java/org/broadinstitute/hellbender/utils/samples/Trio.java
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 src/main/java/org/broadinstitute/hellbender/transformers/NDNCigarReadTransformer.java
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Jobs
ID Job ID Ran Files Coverage
1 2687.1 (CLOUD=mandatory) 0
18.8
 Travis Job 2687.1
Source Files on build 2687
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