broadinstitute / hellbender / 509
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Files 339
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akiezun 
Merge pull request #524 from broadinstitute/lb_update_sam_header

changing dataflow SAM classes to pass around a SAMHeader

20 of 20 new or added lines in 7 files covered. (100.0%)

13415 of 18757 relevant lines covered (71.52%)

0.72 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/PTransformSAM.java
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/ReadsSource.java

Uncovered Existing Lines

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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationTables.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationArgumentCollection.java
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 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportColumn.java
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 src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/BQSRGatherer.java
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 src/main/java/org/broadinstitute/hellbender/tools/SplitReads.java
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 src/main/java/org/broadinstitute/hellbender/utils/text/TextFormattingUtils.java
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 src/main/java/org/broadinstitute/hellbender/utils/codecs/table/TableCodec.java
1
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 src/main/java/org/broadinstitute/hellbender/utils/runtime/OutputStreamSettings.java
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 src/main/java/org/broadinstitute/hellbender/utils/QualityUtils.java
1
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 src/main/java/org/broadinstitute/hellbender/utils/MRUCachingSAMSequenceDictionary.java
1
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 src/main/java/org/broadinstitute/hellbender/engine/filters/ReadFilterLibrary.java
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 src/main/java/org/broadinstitute/hellbender/utils/io/HardThresholdingOutputStream.java
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 src/main/java/org/broadinstitute/hellbender/utils/runtime/InputStreamSettings.java
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/ReadRecalibrationInfo.java
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 src/main/java/org/broadinstitute/hellbender/utils/runtime/ProcessSettings.java
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 src/main/java/org/broadinstitute/hellbender/utils/runtime/StreamOutput.java
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 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportDataType.java
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 src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java
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 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportColumnFormat.java
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 src/main/java/org/broadinstitute/hellbender/utils/runtime/CapturedStreamOutput.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/ContextCovariate.java
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 src/main/java/org/broadinstitute/hellbender/engine/FeatureInput.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/NGSPlatform.java
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 src/main/java/org/broadinstitute/hellbender/tools/examples/PrintReadsWithVariants.java
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 src/main/java/org/broadinstitute/hellbender/utils/MannWhitneyU.java
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 src/main/java/org/broadinstitute/hellbender/utils/collections/NestedIntegerArray.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/QualQuantizer.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/MergeBamAlignment.java
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 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportVersion.java
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 src/main/java/org/broadinstitute/hellbender/utils/GenomeLocSortedSet.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationReport.java
6
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 src/main/java/org/broadinstitute/hellbender/utils/locusiterator/AlignmentStateMachine.java
6
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/FastqToSam.java
6
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 src/main/java/org/broadinstitute/hellbender/transformers/NDNCigarReadTransformer.java
7
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 src/main/java/org/broadinstitute/hellbender/engine/FeatureContext.java
7
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 src/main/java/org/broadinstitute/hellbender/utils/text/XReadLines.java
7
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 src/main/java/org/broadinstitute/hellbender/engine/ReadsDataSource.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/CycleCovariate.java
8
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 src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineProgram.java
8
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/markduplicates/MarkDuplicates.java
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 src/main/java/org/broadinstitute/hellbender/exceptions/GATKException.java
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 src/main/java/org/broadinstitute/hellbender/utils/BaseUtils.java
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 src/main/java/org/broadinstitute/hellbender/tools/ClipReads.java
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 src/main/java/org/broadinstitute/hellbender/tools/FlagStat.java
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 src/main/java/org/broadinstitute/hellbender/utils/haplotype/Haplotype.java
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 src/main/java/org/broadinstitute/hellbender/utils/io/Resource.java
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 src/main/java/org/broadinstitute/hellbender/tools/IndexFeatureFile.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/CompareSAMs.java
13
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 src/main/java/org/broadinstitute/hellbender/utils/GenomeLocParser.java
13
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 src/main/java/org/broadinstitute/hellbender/tools/examples/PrintReadsWithReference.java
14
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 src/main/java/org/broadinstitute/hellbender/utils/IntervalUtils.java
14
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 src/main/java/org/broadinstitute/hellbender/cmdline/ClassFinder.java
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 src/main/java/org/broadinstitute/hellbender/tools/LeftAlignIndels.java
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 src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/BuildBamIndex.java
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 src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/AddOrReplaceReadGroups.java
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 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReport.java
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 src/main/java/org/broadinstitute/hellbender/utils/fasta/CachingIndexedFastaSequenceFile.java
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 src/main/java/org/broadinstitute/hellbender/utils/pileup/PileupElement.java
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/OverhangFixingManager.java
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 src/main/java/org/broadinstitute/hellbender/utils/clipping/ReadClipper.java
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BaseRecalibrator.java
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReads.java
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 src/main/java/org/broadinstitute/hellbender/utils/haplotype/EventMap.java
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/AnalyzeCovariates.java
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 src/main/java/org/broadinstitute/hellbender/utils/R/RScriptExecutor.java
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 src/main/java/org/broadinstitute/hellbender/utils/GenomeLoc.java
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 src/main/java/org/broadinstitute/hellbender/utils/clipping/ClippingOp.java
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 src/main/java/org/broadinstitute/hellbender/Main.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/RevertOriginalBaseQualitiesAndAddMateCigar.java
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 src/main/java/org/broadinstitute/hellbender/utils/Utils.java
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 src/main/java/org/broadinstitute/hellbender/exceptions/UserException.java
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 src/main/java/org/broadinstitute/hellbender/utils/runtime/ProcessController.java
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 src/main/java/org/broadinstitute/hellbender/utils/MathUtils.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/ReorderSam.java
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 src/main/java/org/broadinstitute/hellbender/utils/io/IOUtils.java
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 src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineParser.java
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 src/main/java/org/broadinstitute/hellbender/utils/baq/BAQ.java
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 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportTable.java
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 src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/markduplicates/EstimateLibraryComplexity.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalUtils.java
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 src/main/java/org/broadinstitute/hellbender/utils/iterators/MarkDuplicatesWithMateCigarIterator.java
Jobs
ID Job ID Ran Files Coverage
1 509.1 (TERM=dumb) 0
71.52
 Travis Job 509.1
Source Files on build 509
Detailed source file information is not available for this build.