hammerlab / adam / 53
85%
master: 78%

LAST BUILD BRANCH: 0.23.2
DEFAULT BRANCH: master
Ran
Jobs 7
Files 129
Run time 9min
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53

Pull #12

travis-ci

web-flow 
ContigName Factory fixes, dep cleanups
Pull Request #12: merge in upstream, use hammerlab.paths.Path

1378 of 1378 new or added lines in 53 files covered. (100.0%)

4739 of 5577 relevant lines covered (84.97%)

5.95 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
1
94.27
 2.38% src/main/scala/org/bdgenomics/adam/models/MdTag.scala
1
90.0
 -10.0% src/main/scala/org/bdgenomics/adam/rdd/OutFormatter.scala
1
97.22
 97.22% src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/DinucCovariate.scala
1
87.5
 src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Observation.scala
2
45.45
 -0.26% src/main/scala/org/bdgenomics/adam/rdd/TreeRegionJoin.scala
2
84.91
 -1.09% src/main/scala/org/bdgenomics/adam/rdd/feature/CoverageRDD.scala
2
92.59
 -0.74% src/main/scala/org/bdgenomics/adam/rdd/variant/VariantContextRDD.scala
2
99.2
 -0.8% src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala
3
90.32
 src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/CovariateSpace.scala
3
90.52
 0.41% src/main/scala/org/bdgenomics/adam/util/TwoBitFile.scala
4
85.71
 10.35% src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala
4
92.31
 92.31% src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/BaseQualityRecalibration.scala
5
89.36
 -10.64% src/main/scala/org/bdgenomics/adam/rdd/FileMerger.scala
5
72.86
 0.13% src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDD.scala
5
86.73
 -0.77% src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureRDD.scala
7
95.4
 10.89% src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala
8
0.0
 0.0% src/main/scala/org/bdgenomics/adam/util/ParquetFileTraversable.scala
10
82.76
 82.76% src/main/scala/org/bdgenomics/adam/models/SnpTable.scala
11
69.44
 -30.56% src/main/scala/org/bdgenomics/adam/util/ReferenceContigMap.scala
17
82.08
 0.27% src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala
23
69.57
 -0.99% src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
29
63.75
 src/main/scala/org/bdgenomics/adam/rdd/ParallelFileMerger.scala
56
76.24
 1.6% src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala

Uncovered Existing Lines

Lines Coverage ∆ File
1
82.08
 0.27% src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala
1
82.61
 3.58% src/main/scala/org/bdgenomics/adam/rich/RichAlignmentRecord.scala
1
91.11
 11.11% src/main/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtils.scala
1
64.29
 -7.14% src/main/scala/org/bdgenomics/adam/projections/Projection.scala
1
62.16
 -2.7% src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala
1
96.23
 -1.89% src/main/scala/org/bdgenomics/adam/rdd/read/FlagStat.scala
1
80.0
 0.0% src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala
1
94.27
 2.38% src/main/scala/org/bdgenomics/adam/models/MdTag.scala
1
69.57
 -0.99% src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
1
80.34
 -0.85% src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
1
97.2
 0.0% src/main/scala/org/bdgenomics/adam/rdd/ShuffleRegionJoin.scala
1
84.99
 0.0% src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
1
62.34
 1.3% src/main/scala/org/bdgenomics/adam/rdd/feature/Features.scala
2
57.5
 0.0% src/main/scala/org/bdgenomics/adam/models/RecordGroupDictionary.scala
2
69.23
 0.0% src/main/scala/org/bdgenomics/adam/models/NonoverlappingRegions.scala
2
90.91
 -2.02% src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala
2
88.24
 0.98% src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
3
83.64
 1.82% src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureParser.scala
5
76.24
 1.6% src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
Jobs
ID Job ID Ran Files Coverage
1 53.1 (vars="-Dhadoop.version=2.3.0 -Dspark.version=1.6.3 -DDISABLE_COVERALLS=1") 129
84.97
 Travis Job 53.1
2 53.2 (vars="-Dhadoop.version=2.3.0 -Dspark.version=2.0.2 -DDISABLE_COVERALLS=1") 129
84.97
 Travis Job 53.2
3 53.3 (vars="-Dhadoop.version=2.3.0 -Dspark.version=2.1.0 -DDISABLE_COVERALLS=1") 129
84.97
 Travis Job 53.3
4 53.4 (vars="-Dhadoop.version=2.6.0 -Dspark.version=1.6.3 -DDISABLE_COVERALLS=1") 129
84.97
 Travis Job 53.4
5 53.5 (vars="-Dhadoop.version=2.6.0 -Dspark.version=2.0.2 -DDISABLE_COVERALLS=1") 129
84.97
 Travis Job 53.5
6 53.6 (vars="-Dhadoop.version=2.6.0 -Dspark.version=2.1.0 -DDISABLE_COVERALLS=1") 129
84.97
 Travis Job 53.6
7 53.7 (vars="") 129
84.97
 Travis Job 53.7
Source Files on build 53
Coverage ∆ File Lines Relevant Covered Missed Hits/Line