bigdatagenomics / adam / 1854
81%
master: %

LAST BUILD BRANCH: cli-partition
DEFAULT BRANCH: master
Ran
Jobs 8
Files 132
Run time 42s
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1854

Pull #1423

jenkins

web-flow 
<a href="https://github.com/bigdatagenomics/adam/commit/<a class=hub.com/bigdatagenomics/adam/commit/cc7e0cf5c3acff65c8876c62b7fa198f511122df">cc7e0cf5c<a href="https://github.com/bigdatagenomics/adam/commit/cc7e0cf5c3acff65c8876c62b7fa198f511122df">">Merge </a><a class="double-link" href="https://github.com/bigdatagenomics/adam/commit/<a class="double-link" href="https://github.com/bigdatagenomics/adam/commit/6add9df7032b3caeb5c1da69973cd53969f0484c">6add9df70</a>">6add9df70</a><a href="https://github.com/bigdatagenomics/adam/commit/cc7e0cf5c3acff65c8876c62b7fa198f511122df"> into 07c1982fb">07c1982fb</a>
Pull Request #1423: BQSR refactor for perf improvements

173 of 173 new or added lines in 10 files covered. (100.0%)

4620 of 5747 relevant lines covered (80.39%)

6.42 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
1
91.3
 91.3% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/BaseQualityRecalibration.scala
1
97.22
 97.22% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/DinucCovariate.scala
1
96.55
 96.55% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/ObservationTable.scala
1
97.62
 97.62% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Recalibrator.scala
5
54.44
 -1.7% adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala
10
83.05
 83.05% adam-core/src/main/scala/org/bdgenomics/adam/models/SnpTable.scala

Uncovered Existing Lines

Lines Coverage ∆ File
1
71.43
 -3.57% adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/Consensus.scala
1
94.38
 -1.12% adam-core/src/main/scala/org/bdgenomics/adam/converters/TranscriptEffectConverter.scala
1
91.35
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/models/MdTag.scala
1
90.1
 2.97% adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
1
95.83
 4.17% adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala
1
60.0
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/models/RecordGroupDictionary.scala
1
71.15
 1.92% adam-core/src/main/scala/org/bdgenomics/adam/models/NonoverlappingRegions.scala
1
69.54
 0.51% adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
1
62.16
 -2.7% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala
1
98.11
 -1.89% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/FlagStat.scala
1
97.62
 97.62% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Recalibrator.scala
1
91.3
 91.3% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/BaseQualityRecalibration.scala
1
84.52
 -0.65% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala
2
89.9
 -2.02% adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala
2
93.02
 -2.33% adam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala
2
88.14
 -1.69% adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
2
80.0
 -6.67% adam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala
2
77.94
 -2.94% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala
2
83.49
 0.92% adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureParser.scala
3
73.58
 0.0% adam-cli/src/main/scala/org/bdgenomics/adam/cli/View.scala
3
84.84
 -0.31% adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
3
62.34
 1.3% adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/Features.scala
6
73.45
 -1.03% adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
7
88.71
 9.68% adam-core/src/main/scala/org/bdgenomics/adam/rich/RichAlignmentRecord.scala
12
81.74
 -0.43% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala
22
54.44
 -1.7% adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala
Jobs
ID Job ID Ran Files Coverage
1 1854.1 236
80.27
2 1854.2 236
80.27
3 1854.3 236
80.29
4 1854.4 236
80.29
5 1854.5 236
80.25
6 1854.6 236
80.27
7 1854.7 236
80.25
8 1854.8 236
80.27
Source Files on build 1854
Coverage ∆ File Lines Relevant Covered Missed Hits/Line