broadinstitute / hellbender / 2677
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DEFAULT BRANCH: master
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Jobs 2
Files 523
Run time 1min
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Merge pull request #911 from broadinstitute/dr_lb_spark_bqsr

BQSR on spark

520 of 520 new or added lines in 36 files covered. (100.0%)

21968 of 27324 relevant lines covered (80.4%)

0.97 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
1
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSource.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalOutputSource.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/spark/transforms/ApplyBQSRSparkFn.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/io/IOUtils.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReport.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReferenceDataflowSource.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/BaseRecalibratorDataflow.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/BaseRecalibratorDataflowOptimized.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/spark/BaseRecalibratorSpark.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/ApplyBQSRSpark.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/transforms/BaseRecalibratorSparkFn.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BaseRecalibrator.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorOptimizedTransform.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/utils/recalibration/RecalibrationTables.java
9
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorOptimizedFn.java
16
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSpark.java
23
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/ReadsPreprocessingPipeline.java
23
100.0
 src/main/java/org/broadinstitute/hellbender/utils/recalibration/BaseRecalibrationEngine.java

Uncovered Existing Lines

Lines Coverage ∆ File
1
100.0
 src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/OptionalReferenceInputArgumentCollection.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/BaseRecalibratorDataflow.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/ReadsPreprocessingPipeline.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorOptimizedFn.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSpark.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReport.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportTable.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/io/IOUtils.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSink.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/utils/variant/VariantContextVariantAdapter.java
Jobs
ID Job ID Ran Files Coverage
1 2677.1 (CLOUD=mandatory) 0
18.81
 Travis Job 2677.1
3 2677.3 (CLOUD=false) 0
78.08
 Travis Job 2677.3
Source Files on build 2677
Detailed source file information is not available for this build.