class View extends BDGSparkCommand[ViewArgs]
The adam view
command implements some of the functionality of samtools view
, specifically the -f, -F, -c, and -o
options, in an optionally distributed fashion.
It is agnostic to its input and output being SAM, BAM, or ADAM files; when printing to stdout it prints SAM.
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def
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def
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def
==(arg0: Any): Boolean
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- def applyFilters(reads: RDD[Alignment]): RDD[Alignment]
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val
args: ViewArgs
- Definition Classes
- View → BDGSparkCommand
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final
def
asInstanceOf[T0]: T0
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val
companion: View.type
- Definition Classes
- View → BDGCommand
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def
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def
run(sc: SparkContext): Unit
- Definition Classes
- View → BDGSparkCommand
-
def
run(): Unit
- Definition Classes
- BDGSparkCommand → Runnable
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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(Since version ) see corresponding Javadoc for more information.