bigdatagenomics / adam / 3014

LAST BUILD BRANCH: cli-partition
DEFAULT BRANCH: master
Ran
Jobs 2
Files 6
Run time 7s
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3014

Pull #1895

jenkins

GitHub 
Merge a78508765 into a512113f0
Pull Request #1895: Adding ReadRDD, SequenceRDD, and SliceRDD.

1054 of 1054 new or added lines in 20 files covered. (100.0%)

106 of 128 relevant lines covered (82.81%)

0.83 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
1
91.85
 0.27% adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
1
78.95
 adam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/FlankSlices.scala
2
52.17
 -0.46% adam-apis/src/main/scala/org/bdgenomics/adam/api/java/JavaADAMContext.scala
2
90.91
 adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaSliceConverter.scala
3
11.11
 adam-cli/src/main/scala/org/bdgenomics/adam/cli/CountSliceKmers.scala
3
90.91
 adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaSequenceConverter.scala
3
84.82
 -2.22% adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
6
69.7
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/util/ReferenceContigMap.scala
10
16.67
 adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformSlices.scala
11
15.38
 adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformSequences.scala
26
56.67
 adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ReadDataset.scala
28
68.89
 adam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SequenceDataset.scala
51
0.0
 0.0% adam-apis/src/main/scala/org/bdgenomics/adam/api/java/GenomicDatasetConverters.scala
51
0.0
 0.0% adam-apis/src/main/scala/org/bdgenomics/adam/api/java/GenomicRDDConverters.scala
84
32.26
 adam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SliceDataset.scala
167
76.0
 -16.46% adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala

Uncovered Existing Lines

Lines Coverage ∆ File
1
94.64
 -0.38% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala
1
98.11
 -1.89% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/FlagStat.scala
1
94.19
 -1.16% adam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala
1
96.88
 -3.13% adam-core/src/main/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWaterman.scala
1
92.59
 0.93% adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala
1
84.82
 -2.22% adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
1
63.64
 0.0% adam-cli/src/main/scala/org/bdgenomics/adam/cli/Reads2Coverage.scala
1
90.0
 -1.43% adam-core/src/main/scala/org/bdgenomics/adam/rdd/ShuffleRegionJoin.scala
1
96.63
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/converters/TranscriptEffectConverter.scala
1
84.0
 -1.0% adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/GenotypeDataset.scala
1
81.82
 -9.09% adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala
1
92.86
 -3.57% adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala
2
93.75
 -1.04% adam-core/src/main/scala/org/bdgenomics/adam/models/MdTag.scala
2
80.73
 0.24% adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
2
87.91
 -2.2% adam-core/src/main/scala/org/bdgenomics/adam/util/TwoBitFile.scala
2
85.84
 -0.88% adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureParser.scala
4
60.23
 -1.14% adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/Features.scala
5
59.91
 -2.2% adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala
5
67.27
 -5.45% adam-cli/src/main/scala/org/bdgenomics/adam/cli/View.scala
50
76.0
 -16.46% adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
Jobs
ID Job ID Ran Files Coverage
1 3014.1 146
75.83
2 3014.2 0
Source Files on build 3014