2526

Ran 21 Mar 2017 02:52PM UTC

Jobs 5

Files 0

Run time 18s

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Build # 2526

Build Type

push

jenkins

Committed by

heuermh

Commit Message

[ADAM-1442] Fix thread pool deadlock in GenomicRDD.pipe

Resolves #1442. Eliminates use of thread pool in GenomicRDD and instead launches
the InFormatterRunner (which extends `Callable`) as a thread and runs the
OutFormatterRunner in the original thread that launched the piped subprocess.

Additionally, rewrote the `AnySAMOutFormatter` to improve performance.

Run Details

16 of 16 new or added lines in 2 files covered. (100.0%)

4695 of 5832 relevant lines covered (80.5%)

2.41 hits per line

New Missed Lines in Diff

Lines	Coverage	∆	File
1	100.0		adam-core/src/main/scala/org/bdgenomics/adam/rdd/OutFormatter.scala

Uncovered Existing Lines

Lines	Coverage	File
1	100.0	adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/Consensus.scala
1	100.0	adam-core/src/main/scala/org/bdgenomics/adam/models/NonoverlappingRegions.scala
1	100.0	adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverter.scala
1	100.0	adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala
1	100.0	adam-core/src/main/scala/org/bdgenomics/adam/converters/FastqRecordConverter.scala
1	100.0	adam-core/src/main/scala/org/bdgenomics/adam/models/RecordGroupDictionary.scala
1	100.0	adam-core/src/main/scala/org/bdgenomics/adam/rdd/ShuffleRegionJoin.scala
1	100.0	adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
1	100.0	adam-core/src/main/scala/org/bdgenomics/adam/util/TwoBitFile.scala
1	100.0	adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala
2	100.0	adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala
2	100.0	adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala
2	100.0	adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
2	100.0	adam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala
2	100.0	adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureParser.scala
2	100.0	adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala
3	100.0	adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/Features.scala
4	100.0	adam-core/src/main/scala/org/bdgenomics/adam/converters/TranscriptEffectConverter.scala
5	100.0	adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
7	100.0	adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala

Jobs

ID	Job ID	Ran	Coverage
1	2526.1	21 Mar 2017 02:52PM UTC	80.38
2	2526.2	21 Mar 2017 02:52PM UTC	80.33
3	2526.3	21 Mar 2017 02:52PM UTC	80.38
4	2526.4	21 Mar 2017 02:53PM UTC	80.4
5	2526.5	21 Mar 2017 02:53PM UTC	80.4

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bigdatagenomics / adam / 2526

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