broadinstitute / hellbender / 2709
81%
master: 81%

LAST BUILD BRANCH: dr_disentangle_spark_and_dataflow
DEFAULT BRANCH: master
Ran
Jobs 2
Files 523
Run time 10min
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tomwhite 
Use the sequence dictionary when reading from HDFS if one's available.

6 of 6 new or added lines in 1 file covered. (100.0%)

22096 of 27333 relevant lines covered (80.84%)

0.97 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
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100.0
 src/main/java/htsjdk/samtools/reference/HadoopReferenceSequenceFileFactory.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/engine/spark/JoinReadsWithVariants.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/spark/transforms/markduplicates/MarkDuplicatesSpark.java
1
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 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportTable.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/pipelines/SortBamSpark.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSource.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BaseRecalibrator.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSink.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorFn.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/transformers/BQSRReadTransformer.java
5
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 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReferenceDataflowSource.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/utils/read/SAMRecordToGATKReadAdapter.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/BaseRecalibratorDataflow.java
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 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/BaseRecalibratorDataflowOptimized.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/utils/dataflow/BucketUtils.java
7
100.0
 src/main/java/org/broadinstitute/hellbender/utils/variant/VariantContextVariantAdapter.java
9
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/RefAPISource.java
10
100.0
 src/main/java/htsjdk/samtools/reference/HadoopReferenceSequenceFileFactory.java
10
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorOptimizedTransform.java
12
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/ReadsPreprocessingPipeline.java
15
100.0
 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReport.java
16
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorOptimizedFn.java
16
100.0
 src/main/java/org/broadinstitute/hellbender/utils/dataflow/DataflowUtils.java
17
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSpark.java
24
100.0
 src/main/java/org/broadinstitute/hellbender/utils/read/ReadUtils.java
31
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 src/main/java/org/broadinstitute/hellbender/utils/test/BaseTest.java
35
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 src/main/java/org/broadinstitute/hellbender/utils/baq/BAQ.java
41
100.0
 src/main/java/org/broadinstitute/hellbender/utils/io/IOUtils.java
Jobs
ID Job ID Ran Files Coverage
1 2709.1 (CLOUD=mandatory) 0
18.81
 Travis Job 2709.1
3 2709.3 (CLOUD=false) 0
78.52
 Travis Job 2709.3
Source Files on build 2709
Detailed source file information is not available for this build.