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bigdatagenomics / adam / 3320

Build:
DEFAULT BRANCH: master
Ran 25 Jan 2018 05:42PM UTC
Jobs 2
Files 142
Run time 2min
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[ADAM-1875] Add ability to timeout a piped command.

Resolves #1875. Adds an optional timeout parameter to the `GenomicRDD.pipe`
function. If this is provided, a command will be killed (but without failing the
Spark task) if it runs for longer than the timeout parameter.

6318 of 7639 relevant lines covered (82.71%)

1.65 hits per line

Uncovered Existing Lines

Lines Coverage ∆ File
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adam-cli/src/main/scala/org/bdgenomics/adam/cli/Reads2Coverage.scala
1
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adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala
1
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adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala
1
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adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverter.scala
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adam-core/src/main/scala/org/bdgenomics/adam/models/MdTag.scala
1
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adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala
1
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adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter.scala
1
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adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala
1
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adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala
1
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adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ReferencePositionPair.scala
2
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adam-core/src/main/scala/org/bdgenomics/adam/models/NonoverlappingRegions.scala
2
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adam-core/src/main/scala/org/bdgenomics/adam/models/RecordGroupDictionary.scala
2
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adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
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adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/Features.scala
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adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
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adam-cli/src/main/scala/org/bdgenomics/adam/cli/View.scala
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adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
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adam-core/src/main/scala/org/bdgenomics/adam/rdd/OutFormatter.scala
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adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
Jobs
ID Job ID Ran Files Coverage
1 3320.1 25 Jan 2018 05:42PM UTC 0
82.71
2 3320.2 25 Jan 2018 05:42PM UTC 0
82.71
Source Files on build 3320
Detailed source file information is not available for this build.
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