bigdatagenomics / adam / 2663

DEFAULT BRANCH: master
Ran
Jobs 8
Files 149
Run time 3min
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jenkins

heuermh 
[ADAM-1462] Add quality score binner.

Resolves #1462. Adds an API for binning quality scores to `AlignmentRecordRDD`
and `FragmentRDD`. Exposes this on the `Transform` CLI.

58 of 58 new or added lines in 4 files covered. (100.0%)

5121 of 6244 relevant lines covered (82.01%)

6.55 hits per line

Uncovered Existing Lines

Lines Coverage ∆ File
1
91.11
 -2.22% adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtils.scala
1
56.28
 1.23% adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala
1
66.67
 0.0% adam-cli/src/main/scala/org/bdgenomics/adam/cli/Reads2Coverage.scala
1
92.23
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala
1
89.73
 -0.68% adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
1
62.5
 1.25% adam-core/src/main/scala/org/bdgenomics/adam/models/RecordGroupDictionary.scala
1
86.67
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala
1
64.29
 -7.14% adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala
1
70.5
 0.5% adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
1
77.78
 -5.56% adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter.scala
1
88.35
 0.97% adam-core/src/main/scala/org/bdgenomics/adam/util/TwoBitFile.scala
2
75.93
 1.85% adam-cli/src/main/scala/org/bdgenomics/adam/cli/View.scala
2
96.97
 -1.52% adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverter.scala
2
85.32
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
2
91.67
 -8.33% adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala
2
64.94
 3.9% adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/Features.scala
2
82.19
 -0.09% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala
2
59.46
 -5.41% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala
3
87.13
 -1.98% adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
4
81.65
 -2.75% adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureParser.scala
7
78.55
 -0.75% adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
Jobs
ID Job ID Ran Files Coverage
1 2663.1 251
81.85
2 2663.2 251
81.85
3 2663.3 251
81.87
4 2663.4 251
81.85
5 2663.5 251
81.87
6 2663.6 251
81.87
7 2663.7 251
81.85
8 2663.8 251
81.87
Source Files on build 2663
Coverage ∆ File Lines Relevant Covered Missed Hits/Line