broadinstitute / hellbender / 2587
80%
master: 81%

LAST BUILD BRANCH: dr_disentangle_spark_and_dataflow
DEFAULT BRANCH: master
Ran
Jobs 1
Files 518
Run time 16s
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
2587

push

travis-ci

jean-philippe-martin 
baserecalibrator optimized

692 of 692 new or added lines in 16 files covered. (100.0%)

21171 of 27555 relevant lines covered (76.83%)

0.77 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/SimpleInterval.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/collections/IntervalsSkipList.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/ReadsPreprocessingPipeline.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/RecalibrationEngine.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/read/SAMRecordToGATKReadAdapter.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/DataflowCommandLineProgram.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/utils/collections/IntervalsSkipListOneContig.java
10
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/BaseRecalibratorDataflow.java
11
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorTransform.java
43
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorFn.java
47
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorOptimizedTransform.java
75
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/transforms/composite/AddContextDataToReadOptimized.java
90
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/BaseRecalibratorDataflowOptimized.java
247
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorOptimizedFn.java

Uncovered Existing Lines

Lines Coverage ∆ File
2
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSource.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/SparkContextFactory.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/ReadsPreprocessingPipeline.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/transforms/markduplicates/MarkDuplicatesSpark.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/SimpleInterval.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/SortBamSpark.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BaseRecalibrator.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/utils/baq/BAQ.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/utils/read/SAMRecordToGATKReadAdapter.java
8
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReadsDataflowSource.java
9
100.0
 src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSink.java
13
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/BaseRecalibratorDataflow.java
15
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/RecalibrationEngine.java
16
100.0
 src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSpark.java
17
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/DataflowCommandLineProgram.java
20
100.0
 src/main/java/org/broadinstitute/hellbender/utils/dataflow/SmallBamWriter.java
22
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/ReplaceSamHeader.java
25
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorTransform.java
28
100.0
 src/main/java/org/broadinstitute/hellbender/utils/read/GoogleGenomicsReadToGATKReadAdapter.java
41
100.0
 src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/RefAPISource.java
86
100.0
 src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/bqsr/BaseRecalibratorFn.java
Jobs
ID Job ID Ran Files Coverage
3 2587.3 (CLOUD=false) 0
76.83
 Travis Job 2587.3
Source Files on build 2587
Detailed source file information is not available for this build.