broadinstitute / hellbender / 358
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Jobs 1
Files 338
Run time 25s
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vruano 
Merge pull request #486 from broadinstitute/vrr_mark_duplicates_erc

Adds a couple of read filters to the ExomeReadCounts tool.

5 of 5 new or added lines in 2 files covered. (100.0%)

13313 of 18572 relevant lines covered (71.68%)

0.72 hits per line

Uncovered Existing Lines

Lines Coverage ∆ File
1
100.0
 src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/BQSRGatherer.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/QualityScoreCovariate.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/ReadGroupCovariate.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/RepeatUnitAndLengthCovariate.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/RepeatUnitCovariate.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationTables.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/SplitReads.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/MRUCachingSAMSequenceDictionary.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/QualityUtils.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportColumn.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/runtime/OutputStreamSettings.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/test/ArgumentsBuilder.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/text/TextFormattingUtils.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/engine/ReferenceDataSource.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/io/HardThresholdingOutputStream.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/runtime/InputStreamSettings.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/runtime/ProcessSettings.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/runtime/StreamOutput.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationReport.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportColumnFormat.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/CapturedStreamOutput.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/utils/runtime/RuntimeUtils.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/BaseRecalibration.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/QualQuantizer.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationArgumentCollection.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/utils/collections/NestedIntegerArray.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/utils/MannWhitneyU.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/utils/NGSPlatform.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportVersion.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/transformers/NDNCigarReadTransformer.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/utils/GenomeLocSortedSet.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/utils/io/Resource.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/utils/locusiterator/AlignmentStateMachine.java
7
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/RepeatCovariate.java
7
100.0
 src/main/java/org/broadinstitute/hellbender/utils/text/XReadLines.java
8
100.0
 src/main/java/org/broadinstitute/hellbender/engine/ReadsDataSource.java
8
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/CycleCovariate.java
9
100.0
 src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineProgram.java
9
100.0
 src/main/java/org/broadinstitute/hellbender/exceptions/GATKException.java
9
100.0
 src/main/java/org/broadinstitute/hellbender/utils/haplotype/Haplotype.java
10
100.0
 src/main/java/org/broadinstitute/hellbender/tools/ClipReads.java
10
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/ContextCovariate.java
10
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/AnalyzeCovariates.java
10
100.0
 src/main/java/org/broadinstitute/hellbender/utils/R/RScriptExecutor.java
11
100.0
 src/main/java/org/broadinstitute/hellbender/tools/examples/PrintReadsWithReference.java
11
100.0
 src/main/java/org/broadinstitute/hellbender/tools/FlagStat.java
11
100.0
 src/main/java/org/broadinstitute/hellbender/utils/BaseUtils.java
13
100.0
 src/main/java/org/broadinstitute/hellbender/utils/GenomeLocParser.java
14
100.0
 src/main/java/org/broadinstitute/hellbender/utils/IntervalUtils.java
15
100.0
 src/main/java/org/broadinstitute/hellbender/cmdline/ClassFinder.java
16
100.0
 src/main/java/org/broadinstitute/hellbender/tools/LeftAlignIndels.java
18
100.0
 src/main/java/org/broadinstitute/hellbender/utils/fasta/CachingIndexedFastaSequenceFile.java
18
100.0
 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReport.java
20
100.0
 src/main/java/org/broadinstitute/hellbender/utils/pileup/PileupElement.java
25
100.0
 src/main/java/org/broadinstitute/hellbender/utils/haplotype/EventMap.java
27
100.0
 src/main/java/org/broadinstitute/hellbender/utils/GenomeLoc.java
30
100.0
 src/main/java/org/broadinstitute/hellbender/utils/io/IOUtils.java
31
100.0
 src/main/java/org/broadinstitute/hellbender/Main.java
34
100.0
 src/main/java/org/broadinstitute/hellbender/utils/MathUtils.java
38
100.0
 src/main/java/org/broadinstitute/hellbender/utils/runtime/ProcessController.java
39
100.0
 src/main/java/org/broadinstitute/hellbender/exceptions/UserException.java
41
100.0
 src/main/java/org/broadinstitute/hellbender/utils/Utils.java
48
100.0
 src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineParser.java
53
100.0
 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportTable.java
57
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalUtils.java
69
100.0
 src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
190
100.0
 src/main/java/org/broadinstitute/hellbender/utils/iterators/MarkDuplicatesWithMateCigarIterator.java
Jobs
ID Job ID Ran Files Coverage
1 358.1 (TERM=dumb) 0
71.68
 Travis Job 358.1
Source Files on build 358
Detailed source file information is not available for this build.