• Home
  • Features
  • Pricing
  • Docs
  • Announcements
  • Sign In

broadinstitute / hellbender / 2707
17%
master: 81%

Build:
Build:
LAST BUILD BRANCH: dr_disentangle_spark_and_dataflow
DEFAULT BRANCH: master
Ran 27 Sep 2015 06:10PM UTC
Jobs 1
Files 507
Run time 15s
Badge
Embed â–¾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst

pending completion
2707

push

travis-ci

davidadamsphd
Another small delta.

37 of 37 new or added lines in 2 files covered. (100.0%)

4558 of 26772 relevant lines covered (17.03%)

0.17 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
2
100.0
src/main/java/org/broadinstitute/hellbender/utils/test/BaseTest.java
35
100.0
src/main/java/org/broadinstitute/hellbender/CommandLineProgramTest.java

Uncovered Existing Lines

Lines Coverage ∆ File
1
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/DbsnpArgumentCollection.java
1
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/OptionalVariantInputArgumentCollection.java
1
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineProgramGroup.java
1
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReferenceShard.java
1
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/VariantShard.java
1
100.0
src/main/java/org/broadinstitute/hellbender/engine/filters/VariantFilterLibrary.java
1
100.0
src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorFn.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/RnaSeqMetrics.java
1
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/RrbsCpgDetailMetrics.java
1
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/RrbsSummaryMetrics.java
1
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/InsertSizeMetrics.java
1
100.0
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/recalibration/covariates/ContextCovariate.java
1
100.0
src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/CycleCovariate.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
100.0
src/main/java/org/broadinstitute/hellbender/utils/commandline/Gatherer.java
1
100.0
src/main/java/org/broadinstitute/hellbender/utils/gene/GeneAnnotationReader.java
1
100.0
src/main/java/org/broadinstitute/hellbender/utils/help/HelpConstants.java
1
100.0
src/main/java/org/broadinstitute/hellbender/utils/LoggingUtils.java
1
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/GATKRead.java
1
100.0
src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportColumn.java
2
100.0
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
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/transforms/KeyReadsByRefShard.java
2
100.0
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/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/tools/recalibration/covariates/StandardCovariateList.java
2
100.0
src/main/java/org/broadinstitute/hellbender/tools/recalibration/QuantizationInfo.java
2
100.0
src/main/java/org/broadinstitute/hellbender/utils/gene/LocusFunction.java
2
100.0
src/main/java/org/broadinstitute/hellbender/utils/recalibration/EventType.java
2
100.0
src/main/java/org/broadinstitute/hellbender/utils/R/RScriptExecutorException.java
2
100.0
src/main/java/org/broadinstitute/hellbender/utils/runtime/StreamLocation.java
2
100.0
src/main/java/org/broadinstitute/hellbender/utils/text/XReadLines.java
2
100.0
src/main/java/org/broadinstitute/hellbender/utils/variant/DbSnpVariantType.java
2
100.0
src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java
3
100.0
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
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/QCProgramGroup.java
3
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/ReadProgramGroup.java
3
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/SparkProgramGroup.java
3
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/VariantProgramGroup.java
3
100.0
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
100.0
src/main/java/org/broadinstitute/hellbender/engine/filters/ReadLengthReadFilter.java
3
100.0
src/main/java/org/broadinstitute/hellbender/engine/filters/ReadStrandFilter.java
3
100.0
src/main/java/org/broadinstitute/hellbender/metrics/MultiLevelMetrics.java
3
100.0
src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/CountBasesDataflow.java
3
100.0
src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/FlagStatDataflow.java
3
100.0
src/main/java/org/broadinstitute/hellbender/tools/readersplitters/ReadGroupSplitter.java
3
100.0
src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/ReadGroupCovariate.java
3
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantDatum.java
3
100.0
src/main/java/org/broadinstitute/hellbender/transformers/ReadTransformer.java
3
100.0
src/main/java/org/broadinstitute/hellbender/utils/NGSPlatform.java
3
100.0
src/main/java/org/broadinstitute/hellbender/utils/reference/ReferenceBases.java
3
100.0
src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportDataType.java
3
100.0
src/main/java/org/broadinstitute/hellbender/utils/runtime/StreamOutput.java
4
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/OptionalReferenceInputArgumentCollection.java
4
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/RefAPISource.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/ReadFilter.java
4
100.0
src/main/java/org/broadinstitute/hellbender/engine/filters/ReadGroupReadFilter.java
4
100.0
src/main/java/org/broadinstitute/hellbender/engine/ReferenceDataSource.java
4
100.0
src/main/java/org/broadinstitute/hellbender/engine/spark/GATKRegistrator.java
4
100.0
src/main/java/org/broadinstitute/hellbender/engine/spark/JoinReadsWithRefBases.java
4
100.0
src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/PrintReadsDataflowTransform.java
4
100.0
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
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibratorArgumentCollection.java
4
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/ReadEndsForMarkDuplicates.java
4
100.0
src/main/java/org/broadinstitute/hellbender/utils/samples/Sex.java
4
100.0
src/main/java/org/broadinstitute/hellbender/utils/UnsignedTypeUtil.java
5
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/RequiredIntervalArgumentCollection.java
5
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/RequiredReadInputArgumentCollection.java
5
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/StrictBooleanConverter.java
5
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/PTransformSAM.java
5
100.0
src/main/java/org/broadinstitute/hellbender/engine/filters/FragmentLengthReadFilter.java
5
100.0
src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSource.java
5
100.0
src/main/java/org/broadinstitute/hellbender/tools/CountBases.java
5
100.0
src/main/java/org/broadinstitute/hellbender/tools/CountReads.java
5
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/filter/DepthFilter.java
5
100.0
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
100.0
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
100.0
src/main/java/org/broadinstitute/hellbender/utils/reference/ReferenceUtils.java
5
100.0
src/main/java/org/broadinstitute/hellbender/utils/text/parsers/TabbedInputParser.java
6
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/OptionalReadInputArgumentCollection.java
6
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/RequiredReferenceInputArgumentCollection.java
6
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/DataflowCommandLineProgram.java
6
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReferenceHadoopSource.java
6
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/RefWindowFunctions.java
6
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/transforms/examples/TransformExample.java
6
100.0
src/main/java/org/broadinstitute/hellbender/engine/filters/LibraryReadFilter.java
6
100.0
src/main/java/org/broadinstitute/hellbender/engine/filters/SampleReadFilter.java
6
100.0
src/main/java/org/broadinstitute/hellbender/engine/ReferenceMemorySource.java
6
100.0
src/main/java/org/broadinstitute/hellbender/metrics/SAMRecordAndReference.java
6
100.0
src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/CountBasesDataflowTransform.java
6
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/RrbsMetrics.java
6
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/filter/FisherStrandFilter.java
6
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/GatherVcfs.java
6
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java
6
100.0
src/main/java/org/broadinstitute/hellbender/utils/test/ExomeToolsTestUtils.java
7
100.0
src/main/java/org/broadinstitute/hellbender/engine/spark/JsonSerializer.java
7
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/filter/QdFilter.java
7
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTest.java
7
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/SAMFileGATKReadWriter.java
7
100.0
src/main/java/org/broadinstitute/hellbender/utils/runtime/ProgressLogger.java
7
100.0
src/main/java/org/broadinstitute/hellbender/utils/test/FakeReferenceSource.java
7
100.0
src/main/java/org/broadinstitute/hellbender/utils/text/TextFormattingUtils.java
8
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/PicardCommandLineProgram.java
8
100.0
src/main/java/org/broadinstitute/hellbender/engine/ReferenceFileSource.java
8
100.0
src/main/java/org/broadinstitute/hellbender/engine/spark/JoinReadsWithVariants.java
8
100.0
src/main/java/org/broadinstitute/hellbender/tools/recalibration/ReadCovariates.java
8
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/Coverage.java
8
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityZero.java
8
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/SplitCommonSuffices.java
8
100.0
src/main/java/org/broadinstitute/hellbender/transformers/MisencodedBaseQualityReadTransformer.java
8
100.0
src/main/java/org/broadinstitute/hellbender/utils/io/HardThresholdingOutputStream.java
8
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/CigarConversionUtils.java
8
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/AbstractOpticalDuplicateFinderCommandLineProgram.java
8
100.0
src/main/java/org/broadinstitute/hellbender/utils/runtime/ProcessOutput.java
9
100.0
src/main/java/org/broadinstitute/hellbender/tools/PrintReads.java
9
100.0
src/main/java/org/broadinstitute/hellbender/tools/recalibration/QualQuantizer.java
9
100.0
src/main/java/org/broadinstitute/hellbender/utils/MRUCachingSAMSequenceDictionary.java
9
100.0
src/main/java/org/broadinstitute/hellbender/utils/variant/VariantUtils.java
10
100.0
src/main/java/org/broadinstitute/hellbender/exceptions/GATKException.java
10
100.0
src/main/java/org/broadinstitute/hellbender/utils/runtime/RuntimeUtils.java
11
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineProgram.java
11
100.0
src/main/java/org/broadinstitute/hellbender/engine/ReadsContext.java
11
100.0
src/main/java/org/broadinstitute/hellbender/tools/ApplyBQSR.java
11
100.0
src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/FlagStatusDataflowTransform.java
11
100.0
src/main/java/org/broadinstitute/hellbender/tools/exome/TargetCollections.java
11
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java
11
100.0
src/main/java/org/broadinstitute/hellbender/utils/io/Resource.java
11
100.0
src/main/java/org/broadinstitute/hellbender/utils/R/RScriptLibrary.java
12
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/DataFlowReadFn.java
12
100.0
src/main/java/org/broadinstitute/hellbender/engine/filters/PlatformReadFilter.java
12
100.0
src/main/java/org/broadinstitute/hellbender/engine/filters/PlatformUnitReadFilter.java
12
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/AddCommentsToBam.java
12
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/CompareSAMs.java
12
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ChromosomeCounts.java
12
100.0
src/main/java/org/broadinstitute/hellbender/utils/genotyper/IndexedSampleList.java
12
100.0
src/main/java/org/broadinstitute/hellbender/utils/test/ArgumentsBuilder.java
13
100.0
src/main/java/org/broadinstitute/hellbender/CommandLineProgramTest.java
13
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReadContextData.java
13
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReferenceFileSource.java
13
100.0
src/main/java/org/broadinstitute/hellbender/engine/IntervalWalker.java
13
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/GatherBamFiles.java
13
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTest.java
13
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/MergeTails.java
13
100.0
src/main/java/org/broadinstitute/hellbender/utils/samples/Sample.java
14
100.0
src/main/java/htsjdk/samtools/reference/HadoopFastaSequenceIndexEntry.java
14
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/SamFormatConverter.java
14
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/ByIntervalListVariantContextIterator.java
14
100.0
src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationReport.java
14
100.0
src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationTables.java
14
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/SeqVertex.java
14
100.0
src/main/java/org/broadinstitute/hellbender/utils/genotyper/IndexedAlleleList.java
14
100.0
src/main/java/org/broadinstitute/hellbender/utils/runtime/InputStreamSettings.java
15
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/coders/PairedEndsCoder.java
15
100.0
src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/markduplicates/MarkDuplicates.java
15
100.0
src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/markduplicates/ReadsKey.java
15
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordanceContingencyMetrics.java
15
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/SampleList.java
15
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/TandemRepeat.java
15
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyResult.java
15
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/GraphUtils.java
15
100.0
src/main/java/org/broadinstitute/hellbender/utils/iterators/ByteArrayIterator.java
16
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/Transition.java
16
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/RecalibrationEngine.java
16
100.0
src/main/java/org/broadinstitute/hellbender/utils/codecs/table/TableFeature.java
16
100.0
src/main/java/org/broadinstitute/hellbender/utils/illumina/IlluminaAdapterPair.java
16
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/ReadCoordinateComparator.java
16
100.0
src/main/java/org/broadinstitute/hellbender/utils/samples/Trio.java
17
100.0
src/main/java/org/broadinstitute/hellbender/engine/ReadWalker.java
17
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/GenotypeSummaries.java
17
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatio.java
18
100.0
src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/markduplicates/MarkDuplicatesDataflow.java
18
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordanceSummaryMetrics.java
18
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
18
100.0
src/main/java/org/broadinstitute/hellbender/transformers/NDNCigarReadTransformer.java
18
100.0
src/main/java/org/broadinstitute/hellbender/utils/dataflow/BucketUtils.java
19
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java
19
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/VertexBasedTransformer.java
19
100.0
src/main/java/org/broadinstitute/hellbender/transformers/BQSRReadTransformer.java
19
100.0
src/main/java/org/broadinstitute/hellbender/utils/QualityUtils.java
19
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/ArtificialReadQueryIterator.java
19
100.0
src/main/java/org/broadinstitute/hellbender/utils/runtime/OutputStreamSettings.java
20
100.0
src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSource.java
20
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrand.java
20
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java
20
100.0
src/main/java/org/broadinstitute/hellbender/utils/genotyper/MostLikelyAllele.java
20
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/DiskBasedReadEndsForMarkDuplicatesMap.java
21
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/CleanSam.java
21
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/RenameSampleInVcf.java
22
100.0
src/main/java/org/broadinstitute/hellbender/tools/exome/Sample.java
22
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/filter/AlleleBalanceFilter.java
22
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ActivityProfileState.java
22
100.0
src/main/java/org/broadinstitute/hellbender/utils/codecs/table/TableCodec.java
22
100.0
src/main/java/org/broadinstitute/hellbender/utils/pairhmm/N2MemoryPairHMM.java
23
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/IntervalArgumentCollection.java
23
100.0
src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationArgumentCollection.java
23
100.0
src/main/java/org/broadinstitute/hellbender/utils/IndexRange.java
23
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/ReadEnds.java
24
100.0
src/main/java/org/broadinstitute/hellbender/engine/ReadsDataSource.java
24
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectInsertSizeMetrics.java
24
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySample.java
25
100.0
src/main/java/org/broadinstitute/hellbender/engine/VariantWalker.java
25
100.0
src/main/java/org/broadinstitute/hellbender/tools/examples/PrintReadsWithVariants.java
25
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/interval/LiftOverIntervalList.java
25
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualitySumPerAlleleBySample.java
25
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/MergeDiamonds.java
25
100.0
src/main/java/org/broadinstitute/hellbender/utils/dataflow/DataflowUtils.java
26
100.0
src/main/java/org/broadinstitute/hellbender/engine/filters/CountingReadFilter.java
26
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectAlignmentSummaryMetrics.java
26
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java
26
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReads.java
26
100.0
src/main/java/org/broadinstitute/hellbender/utils/dataflow/SmallBamWriter.java
26
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/BestMapqPrimaryAlignmentSelectionStrategy.java
26
100.0
src/main/java/org/broadinstitute/hellbender/utils/variant/SkeletonVariant.java
26
100.0
src/main/java/org/broadinstitute/hellbender/utils/variant/VariantContextVariantAdapter.java
27
100.0
src/main/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSpark.java
27
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/filter/FilterVcf.java
27
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/BaseEdge.java
27
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/EarliestFragmentPrimaryAlignmentSelectionStrategy.java
28
100.0
src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/markduplicates/PairedEnds.java
28
100.0
src/main/java/org/broadinstitute/hellbender/utils/pairhmm/LoglessPairHMM.java
28
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/BestEndMapqPrimaryAlignmentStrategy.java
29
100.0
src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSink.java
30
100.0
src/main/java/htsjdk/samtools/reference/HadoopFastaSequenceIndex.java
30
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/BaseVertex.java
31
100.0
src/main/java/org/broadinstitute/hellbender/utils/FisherExactTest.java
32
100.0
src/main/java/org/broadinstitute/hellbender/tools/examples/ExampleIntervalWalker.java
32
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/CollectRnaSeqMetrics.java
32
100.0
src/main/java/org/broadinstitute/hellbender/utils/BaseUtils.java
32
100.0
src/main/java/org/broadinstitute/hellbender/utils/genotyper/SampleList.java
32
100.0
src/main/java/org/broadinstitute/hellbender/utils/runtime/ProcessSettings.java
33
100.0
src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/DataflowReadsPipeline.java
33
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java
34
100.0
src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalDatum.java
34
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java
34
100.0
src/main/java/org/broadinstitute/hellbender/utils/variant/DbSnpBitSetUtil.java
35
100.0
src/main/java/org/broadinstitute/hellbender/engine/FeatureContext.java
35
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/AddOrReplaceReadGroups.java
35
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/CreateSequenceDictionary.java
35
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/SplitVcfs.java
35
100.0
src/main/java/org/broadinstitute/hellbender/tools/recalibration/BQSRGatherer.java
36
100.0
src/main/java/org/broadinstitute/hellbender/engine/dataflow/transforms/RemoveDuplicateReadVariantPairs.java
36
100.0
src/main/java/org/broadinstitute/hellbender/engine/ReferenceContext.java
36
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java
36
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/LibraryIdGenerator.java
36
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/ReadEndsForMarkDuplicatesCodec.java
37
100.0
src/main/java/org/broadinstitute/hellbender/engine/FeatureInput.java
37
100.0
src/main/java/org/broadinstitute/hellbender/tools/exome/TargetCollection.java
37
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/interval/BedToIntervalList.java
37
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/filter/FilterApplyingVariantIterator.java
37
100.0
src/main/java/org/broadinstitute/hellbender/utils/runtime/CapturedStreamOutput.java
37
100.0
src/main/java/org/broadinstitute/hellbender/utils/text/parsers/TabbedTextFileWithHeaderParser.java
38
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/PossibleDeNovo.java
38
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepth.java
38
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RankSumTest.java
38
100.0
src/main/java/org/broadinstitute/hellbender/utils/report/GATKReport.java
38
100.0
src/main/java/org/broadinstitute/hellbender/utils/SimpleInterval.java
39
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/ValidateSamFile.java
40
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/SequencingArtifactMetrics.java
40
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/DuplicationMetrics.java
41
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/SinglePassSamProgram.java
41
100.0
src/main/java/org/broadinstitute/hellbender/utils/test/ReadClipperTestUtils.java
42
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/QualityScoreDistribution.java
42
100.0
src/main/java/org/broadinstitute/hellbender/utils/pairhmm/LogPairHMM.java
43
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/Kmer.java
45
100.0
src/main/java/org/broadinstitute/hellbender/tools/SplitReads.java
45
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/OxoGReadCounts.java
45
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java
46
100.0
src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportTable.java
46
100.0
src/main/java/org/broadinstitute/hellbender/utils/SequenceDictionaryUtils.java
47
100.0
src/main/java/htsjdk/samtools/reference/HadoopReferenceSequenceFileFactory.java
47
100.0
src/main/java/org/broadinstitute/hellbender/utils/clipping/ReadClipper.java
47
100.0
src/main/java/org/broadinstitute/hellbender/utils/text/parsers/BasicInputParser.java
48
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/MergeBamAlignment.java
48
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/MergeSamFiles.java
49
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectQualityYieldMetrics.java
50
100.0
src/main/java/org/broadinstitute/hellbender/engine/filters/ReadGroupBlackListReadFilter.java
50
100.0
src/main/java/org/broadinstitute/hellbender/exceptions/UserException.java
50
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/interval/IntervalListScatterer.java
50
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordanceScheme.java
50
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantOverlapAnnotator.java
50
100.0
src/main/java/org/broadinstitute/hellbender/utils/samples/MendelianViolation.java
50
100.0
src/main/java/org/broadinstitute/hellbender/utils/text/parsers/AbstractInputParser.java
52
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/ArtificialReadIterator.java
53
100.0
src/main/java/org/broadinstitute/hellbender/utils/collections/CountSet.java
56
100.0
src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java
56
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/CollectRrbsMetrics.java
56
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/InbreedingCoeff.java
56
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java
57
100.0
src/main/java/org/broadinstitute/hellbender/utils/fasta/CachingIndexedFastaSequenceFile.java
58
100.0
src/main/java/org/broadinstitute/hellbender/utils/gene/Gene.java
59
100.0
src/main/java/org/broadinstitute/hellbender/utils/locusiterator/AlignmentStateMachine.java
60
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ValidateVariants.java
60
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/MultiHitAlignedReadIterator.java
63
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandBiasTest.java
63
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
64
100.0
src/main/java/org/broadinstitute/hellbender/tools/exome/SampleCollection.java
64
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/Path.java
65
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/ContextAccumulator.java
65
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/SortVcf.java
65
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java
65
100.0
src/main/java/org/broadinstitute/hellbender/utils/haplotype/Haplotype.java
66
100.0
src/main/java/org/broadinstitute/hellbender/utils/pileup/ReadPileup.java
68
100.0
src/main/java/org/broadinstitute/hellbender/Main.java
68
100.0
src/main/java/org/broadinstitute/hellbender/utils/genotyper/AlleleList.java
69
100.0
src/main/java/org/broadinstitute/hellbender/utils/pileup/PileupElement.java
71
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/MeanQualityByCycle.java
72
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/OpticalDuplicateFinder.java
73
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordanceStates.java
75
100.0
src/main/java/org/broadinstitute/hellbender/utils/GenomeLocParser.java
76
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/OverhangFixingManager.java
77
100.0
src/main/java/org/broadinstitute/hellbender/utils/gene/RefFlatReader.java
77
100.0
src/main/java/org/broadinstitute/hellbender/utils/genotyper/PerReadAlleleLikelihoodMap.java
78
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/SeqGraph.java
78
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/readthreading/TestingReadThreadingGraph.java
78
100.0
src/main/java/org/broadinstitute/hellbender/utils/downsampling/AlleleBiasedDownsamplingUtils.java
78
100.0
src/main/java/org/broadinstitute/hellbender/utils/test/BaseTest.java
79
100.0
src/main/java/org/broadinstitute/hellbender/utils/io/IOUtils.java
79
100.0
src/main/java/org/broadinstitute/hellbender/utils/MannWhitneyU.java
80
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordanceCounts.java
80
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/MostDistantPrimaryAlignmentSelectionStrategy.java
81
100.0
src/main/java/org/broadinstitute/hellbender/metrics/MultiLevelCollector.java
81
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/HitsForInsert.java
81
100.0
src/main/java/org/broadinstitute/hellbender/utils/R/RScriptExecutor.java
82
100.0
src/main/java/org/broadinstitute/hellbender/utils/collections/IndexedSet.java
85
100.0
src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java
85
100.0
src/main/java/org/broadinstitute/hellbender/tools/FlagStat.java
86
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/AnalyzeCovariates.java
87
100.0
src/main/java/org/broadinstitute/hellbender/utils/pairhmm/PairHMMModel.java
90
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectBaseDistributionByCycle.java
91
100.0
src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java
93
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/RevertSam.java
94
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/ArtificialReadUtils.java
95
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/InsertSizeMetricsCollector.java
96
100.0
src/main/java/org/broadinstitute/hellbender/utils/pairhmm/PairHMM.java
99
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
100
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/CollectSequencingArtifactMetrics.java
105
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyResultSet.java
106
100.0
src/main/java/org/broadinstitute/hellbender/tools/exome/HashedListTargetCollection.java
106
100.0
src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalUtils.java
108
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/Tranche.java
108
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/SamAlignmentMerger.java
109
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/GoogleGenomicsReadToGATKReadAdapter.java
110
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/ArtifactCounter.java
110
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/AbstractMarkDuplicatesCommandLineProgram.java
110
100.0
src/main/java/org/broadinstitute/hellbender/utils/runtime/ProcessController.java
111
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyRegion.java
111
100.0
src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java
114
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/SamComparison.java
118
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/filters/VariantFiltration.java
119
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/RrbsMetricsCollector.java
121
100.0
src/main/java/org/broadinstitute/hellbender/utils/GenomeLocSortedSet.java
122
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java
122
100.0
src/main/java/org/broadinstitute/hellbender/utils/GenomeLoc.java
134
100.0
src/main/java/org/broadinstitute/hellbender/utils/clipping/ClippingOp.java
135
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/ReadUtils.java
136
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/CigarUtils.java
137
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
137
100.0
src/main/java/org/broadinstitute/hellbender/utils/MathUtils.java
138
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/FastqToSam.java
144
100.0
src/main/java/org/broadinstitute/hellbender/utils/haplotype/EventMap.java
147
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/SamToFastq.java
162
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/RnaSeqMetricsCollector.java
162
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
170
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/SAMRecordToGATKReadAdapter.java
172
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BaseRecalibrator.java
179
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/AlignmentSummaryMetricsCollector.java
181
100.0
src/main/java/org/broadinstitute/hellbender/tools/exome/ExomeReadCounts.java
187
100.0
src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineParser.java
199
100.0
src/main/java/org/broadinstitute/hellbender/tools/ClipReads.java
204
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordance.java
207
100.0
src/main/java/org/broadinstitute/hellbender/utils/smithwaterman/SWPairwiseAlignment.java
211
100.0
src/main/java/org/broadinstitute/hellbender/utils/Utils.java
215
100.0
src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/markduplicates/MarkDuplicatesUtils.java
238
100.0
src/main/java/org/broadinstitute/hellbender/tools/picard/sam/markduplicates/MarkDuplicates.java
238
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/BaseGraph.java
261
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/AbstractAlignmentMerger.java
356
100.0
src/main/java/org/broadinstitute/hellbender/utils/read/AlignmentUtils.java
357
100.0
src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
374
100.0
src/main/java/org/broadinstitute/hellbender/utils/IntervalUtils.java
405
100.0
src/main/java/org/broadinstitute/hellbender/utils/genotyper/ReadLikelihoods.java
415
100.0
src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
Jobs
ID Job ID Ran Files Coverage
1 2707.1 (CLOUD=mandatory) 27 Sep 2015 06:10PM UTC 0
17.03
Travis Job 2707.1
Source Files on build 2707
Detailed source file information is not available for this build.
  • Back to Repo
  • Travis Build #2707
  • b5b02c4f on github
  • Prev Build on da_spark_integration (#2378)
STATUS · Troubleshooting · Open an Issue · Sales · Support · CAREERS · ENTERPRISE · START FREE · SCHEDULE DEMO
ANNOUNCEMENTS · TWITTER · TOS & SLA · Supported CI Services · What's a CI service? · Automated Testing

© 2025 Coveralls, Inc