broadinstitute / hellbender / 2649
80%
master: 81%

LAST BUILD BRANCH: dr_disentangle_spark_and_dataflow
DEFAULT BRANCH: master
Ran
Jobs 1
Files 523
Run time 18s
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travis-ci

droazen 
BQSR on spark

-Ported BQSR and ApplyBQSR to spark.

-Refactored the BQSR engine so that all versions of BQSR (walker, dataflow,
 and spark) call into a common engine, and removed duplicated versions
 of the engine from the codebase.

519 of 519 new or added lines in 36 files covered. (100.0%)

21184 of 27308 relevant lines covered (77.57%)

0.78 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
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 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalOutputSource.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/read/SAMRecordToGATKReadAdapter.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReport.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/dataflow/BucketUtils.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReferenceDataflowSource.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/SparkCommandLineProgram.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/ApplyBQSRSpark.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BaseRecalibrator.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/utils/read/ReadUtils.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/utils/recalibration/RecalibrationTables.java
8
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorOptimizedTransform.java
8
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorTransform.java
13
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/transforms/BaseRecalibratorSparkFn.java
14
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorFn.java
16
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSpark.java
18
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorOptimizedFn.java
23
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/ReadsPreprocessingPipeline.java
24
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 src/main/java/org/broadinstitute/hellbender/utils/recalibration/BaseRecalibrationEngine.java
28
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/BaseRecalibratorDataflow.java
30
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 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/BaseRecalibratorDataflowOptimized.java
34
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/BaseRecalibratorSpark.java

Uncovered Existing Lines

Lines Coverage ∆ File
1
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSink.java
1
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 src/main/java/org/broadinstitute/hellbender/engine/spark/JoinReadsWithVariants.java
1
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 src/main/java/org/broadinstitute/hellbender/utils/recalibration/QuantizationInfo.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/recalibration/RecalibrationArgumentCollection.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorTransform.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSource.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/ReadsPreprocessingPipeline.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/transformers/BQSRReadTransformer.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/utils/variant/VariantContextVariantAdapter.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/utils/recalibration/RecalibrationTables.java
8
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReferenceDataflowSource.java
8
100.0
 src/main/java/org/broadinstitute/hellbender/utils/read/SAMRecordToGATKReadAdapter.java
9
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSpark.java
10
100.0
 src/main/java/org/broadinstitute/hellbender/utils/recalibration/RecalibrationReport.java
12
100.0
 src/main/java/org/broadinstitute/hellbender/utils/dataflow/BucketUtils.java
15
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorOptimizedTransform.java
15
100.0
 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReport.java
21
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorFn.java
23
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/BaseRecalibratorDataflowOptimized.java
23
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorOptimizedFn.java
23
100.0
 src/main/java/org/broadinstitute/hellbender/utils/dataflow/DataflowUtils.java
23
100.0
 src/main/java/org/broadinstitute/hellbender/utils/read/ReadUtils.java
28
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/BaseRecalibratorDataflow.java
35
100.0
 src/main/java/org/broadinstitute/hellbender/utils/baq/BAQ.java
40
100.0
 src/main/java/org/broadinstitute/hellbender/utils/io/IOUtils.java
40
100.0
 src/main/java/org/broadinstitute/hellbender/utils/test/BaseTest.java
43
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/RefAPISource.java
56
100.0
 src/main/java/org/broadinstitute/hellbender/utils/recalibration/RecalUtils.java
Jobs
ID Job ID Ran Files Coverage
3 2649.3 (CLOUD=false) 0
77.57
 Travis Job 2649.3
Source Files on build 2649
Detailed source file information is not available for this build.