bigdatagenomics / adam / 1848
81%
master: %

LAST BUILD BRANCH: cli-partition
DEFAULT BRANCH: master
Ran
Jobs 8
Files 132
Run time 1min
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1848

Pull #1423

jenkins

web-flow 
<a href="https://github.com/bigdatagenomics/adam/commit/<a class=hub.com/bigdatagenomics/adam/commit/ea26d28f1a1c00f3707be2941c6f6a68e7773aa9">ea26d28f1<a href="https://github.com/bigdatagenomics/adam/commit/ea26d28f1a1c00f3707be2941c6f6a68e7773aa9">">Merge </a><a class="double-link" href="https://github.com/bigdatagenomics/adam/commit/<a class="double-link" href="https://github.com/bigdatagenomics/adam/commit/0e4863b60f5d6168c457e05113f444aa1159da07">0e4863b60</a>">0e4863b60</a><a href="https://github.com/bigdatagenomics/adam/commit/ea26d28f1a1c00f3707be2941c6f6a68e7773aa9"> into 07c1982fb">07c1982fb</a>
Pull Request #1423: BQSR refactor for perf improvements

169 of 169 new or added lines in 10 files covered. (100.0%)

4614 of 5729 relevant lines covered (80.54%)

6.43 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
1
95.83
 95.83% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/BaseQualityRecalibration.scala
1
98.81
 98.81% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Recalibrator.scala
3
78.57
 78.57% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/CycleCovariate.scala
3
89.19
 89.19% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/DinucCovariate.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
75.0
 0.0% adam-cli/src/main/scala/org/bdgenomics/adam/cli/Reads2Coverage.scala
1
89.11
 1.98% adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
1
88.98
 -0.85% adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
1
60.0
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/models/RecordGroupDictionary.scala
1
98.11
 -1.89% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/FlagStat.scala
1
95.24
 95.24% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Covariate.scala
1
76.36
 34.55% adam-core/src/main/scala/org/bdgenomics/adam/rich/DecadentRead.scala
1
88.64
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/util/TwoBitFile.scala
1
94.74
 94.74% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/ObservationTable.scala
1
62.16
 -2.7% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala
1
93.33
 6.67% adam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala
1
95.83
 4.17% adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala
1
92.43
 1.08% adam-core/src/main/scala/org/bdgenomics/adam/models/MdTag.scala
2
84.99
 -0.15% adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
2
94.38
 -1.12% adam-core/src/main/scala/org/bdgenomics/adam/converters/TranscriptEffectConverter.scala
2
93.02
 -2.33% adam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala
2
69.04
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
2
62.34
 1.3% adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/Features.scala
2
82.57
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureParser.scala
2
77.94
 -2.94% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala
2
90.91
 -1.01% adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala
2
75.47
 1.89% adam-cli/src/main/scala/org/bdgenomics/adam/cli/View.scala
5
75.26
 0.77% 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 1848.1 235
80.38
2 1848.2 235
80.38
3 1848.3 235
80.4
4 1848.4 235
80.42
5 1848.5 235
80.4
6 1848.6 235
80.4
7 1848.7 235
80.4
8 1848.8 235
80.42
Source Files on build 1848
Coverage ∆ File Lines Relevant Covered Missed Hits/Line