Class/Object

org.bdgenomics.adam.cli

View

Related Docs: object View | package cli

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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.

Linear Supertypes
BDGSparkCommand[ViewArgs], Logging, BDGCommand, Runnable, AnyRef, Any
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Inherited
  1. View
  2. BDGSparkCommand
  3. Logging
  4. BDGCommand
  5. Runnable
  6. AnyRef
  7. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new View(args: ViewArgs)

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Type Members

  1. type ReadFilter = (AlignmentRecord) ⇒ Boolean

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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  4. def applyFilters(reads: RDD[AlignmentRecord]): RDD[AlignmentRecord]

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  5. val args: ViewArgs

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    Definition Classes
    View → BDGSparkCommand

  6. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  7. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  8. val companion: View.type

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    Definition Classes
    View → BDGCommand

  9. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  10. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  11. def debug(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  12. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  13. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  14. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  15. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  16. def error(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  17. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  18. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  19. def getFilters(n: Int, matchValue: Boolean = true): List[ReadFilter]

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  20. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  21. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  22. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  23. def info(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  24. def initializeMetrics(sc: SparkContext): Option[MetricsListener]

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    Definition Classes
    BDGSparkCommand

  25. def isDebugEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  26. def isErrorEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  27. def isInfoEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  28. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  29. def isTraceEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  30. def isWarnEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  31. def logger: Logger

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    Attributes
    protected
    Definition Classes
    Logging

  32. def loggerName: String

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    Attributes
    protected
    Definition Classes
    Logging

  33. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  34. final def notify(): Unit

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    Definition Classes
    AnyRef

  35. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  36. def printMetrics(totalTime: Long, metricsListener: Option[MetricsListener]): Unit

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    Definition Classes
    BDGSparkCommand

  37. def run(sc: SparkContext): Unit

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    Definition Classes
    View → BDGSparkCommand

  38. def run(): Unit

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    Definition Classes
    BDGSparkCommand → Runnable

  39. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef

  40. def toString(): String

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    Definition Classes
    AnyRef → Any

  41. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  42. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  43. def trace(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  44. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  45. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  46. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  47. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  48. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  49. def warn(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

Inherited from BDGSparkCommand[ViewArgs]

Inherited from Logging

Inherited from BDGCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

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