bigdatagenomics / adam / 2813

DEFAULT BRANCH: master
Ran
Jobs 8
Files 154
Run time 2min
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2813

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jenkins

heuermh 
[ADAM-1438] Add ability to save FASTA back as a single file.

Resolves #1438. To support saving FASTA as a single file, moved the
private `writeTextRdd` method from the `FeatureRDD` to `GenomicRDD`, and opened
protections to `protected`.

14 of 14 new or added lines in 2 files covered. (100.0%)

5737 of 6833 relevant lines covered (83.96%)

6.69 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
1
72.73
 -0.84% adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDD.scala

Uncovered Existing Lines

Lines Coverage ∆ File
1
95.35
 -1.16% adam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala
1
94.27
 -0.52% adam-core/src/main/scala/org/bdgenomics/adam/models/MdTag.scala
1
95.83
 -4.17% adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala
1
89.81
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
1
67.31
 -1.92% adam-core/src/main/scala/org/bdgenomics/adam/models/NonoverlappingRegions.scala
1
93.33
 -6.67% adam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala
1
91.51
 0.69% adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
1
72.73
 -0.84% adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDD.scala
1
86.24
 0.92% adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureParser.scala
1
81.23
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala
1
82.54
 -1.59% adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala
2
60.49
 -1.23% adam-core/src/main/scala/org/bdgenomics/adam/models/RecordGroupDictionary.scala
2
64.94
 0.0% adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/Features.scala
3
59.9
 -1.52% adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala
3
72.22
 -1.85% adam-cli/src/main/scala/org/bdgenomics/adam/cli/View.scala
3
81.91
 -0.14% adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
3
89.32
 -1.94% adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
4
94.38
 -4.49% adam-core/src/main/scala/org/bdgenomics/adam/converters/TranscriptEffectConverter.scala
8
88.37
 0.42% adam-core/src/main/scala/org/bdgenomics/adam/converters/FastqRecordConverter.scala
Jobs
ID Job ID Ran Files Coverage
1 2813.1 154
83.69
2 2813.2 154
83.69
3 2813.3 154
83.62
4 2813.4 154
83.62
5 2813.5 154
83.64
6 2813.6 154
83.68
7 2813.7 154
83.68
8 2813.8 154
83.64
Source Files on build 2813
Coverage ∆ File Lines Relevant Covered Missed Hits/Line