broadinstitute / hellbender / 179
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Files 120
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akiezun 
Merge pull request #119 from broadinstitute/ak_analyzeCovariates

analyze covariates part1

2715 of 2715 new or added lines in 51 files covered. (100.0%)

6293 of 10383 relevant lines covered (60.61%)

0.61 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
1
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 src/main/java/org/broadinstitute/hellbender/tools/SplitNCigarReads.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalDatum.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/RepeatLengthCovariate.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/RepeatUnitAndLengthCovariate.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/RepeatUnitCovariate.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/StreamOutput.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/QualityScoreCovariate.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/ReadGroupCovariate.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/utils/runtime/CapturedStreamOutput.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/utils/sam/ArtificialSAMUtils.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/utils/NGSPlatform.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/utils/Utils.java
4
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 src/main/java/org/broadinstitute/hellbender/utils/collections/NestedIntegerArray.java
7
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationTables.java
8
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 src/main/java/org/broadinstitute/hellbender/utils/runtime/ProcessSettings.java
10
100.0
 src/main/java/org/broadinstitute/hellbender/utils/runtime/RuntimeUtils.java
14
100.0
 src/main/java/org/broadinstitute/hellbender/utils/sam/ReadUtils.java
15
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/RepeatCovariate.java
15
100.0
 src/main/java/org/broadinstitute/hellbender/utils/R/RUtils.java
22
100.0
 src/main/java/org/broadinstitute/hellbender/exceptions/UserException.java
22
100.0
 src/main/java/org/broadinstitute/hellbender/utils/io/IOUtils.java
22
100.0
 src/main/java/org/broadinstitute/hellbender/utils/runtime/OutputStreamSettings.java
24
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 src/main/java/org/broadinstitute/hellbender/utils/io/Resource.java
25
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/ContextCovariate.java
27
100.0
 src/main/java/org/broadinstitute/hellbender/utils/R/RScriptExecutor.java
27
100.0
 src/main/java/org/broadinstitute/hellbender/utils/runtime/InputStreamSettings.java
30
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/QuantizationInfo.java
30
100.0
 src/main/java/org/broadinstitute/hellbender/utils/MannWhitneyU.java
36
100.0
 src/main/java/org/broadinstitute/hellbender/utils/collections/LoggingNestedIntegerArray.java
37
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/BQSRGatherer.java
47
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/BaseRecalibration.java
47
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/QualQuantizer.java
53
100.0
 src/main/java/org/broadinstitute/hellbender/utils/runtime/ProcessController.java
75
100.0
 src/main/java/org/broadinstitute/hellbender/utils/classloader/JVMUtils.java
76
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/CycleCovariate.java
90
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationArgumentCollection.java
102
100.0
 src/main/java/org/broadinstitute/hellbender/utils/classloader/PluginManager.java
112
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/AnalyzeCovariates.java
159
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationReport.java
324
100.0
 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalUtils.java

Uncovered Existing Lines

Lines Coverage ∆ File
1
100.0
 src/main/java/org/broadinstitute/hellbender/exceptions/UserException.java
Jobs
ID Job ID Ran Files Coverage
1 179.1 (TERM=dumb) 0
60.61
 Travis Job 179.1
Source Files on build 179
Detailed source file information is not available for this build.