org.bdgenomics.adam.cli

View

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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Instance Constructors

  1. new View(args: ViewArgs)

Type Members

  1. type ReadFilter = (AlignmentRecord) ⇒ Boolean

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

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

  7. val args: ViewArgs

    Definition Classes
    View → BDGSparkCommand

  8. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  9. def clone(): AnyRef

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

  10. val companion: View.type

    Definition Classes
    View → BDGCommand

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

    Definition Classes
    AnyRef

  12. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  13. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  15. def getFilters(n: Int, matchValue: Boolean = true): List[(AlignmentRecord) ⇒ Boolean]

  16. def hashCode(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    BDGSparkCommand

  18. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  19. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging

  20. def log: Logger

    Attributes
    protected
    Definition Classes
    Logging

  21. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  22. def logDebug(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  23. def logError(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  24. def logError(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  25. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  26. def logInfo(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  27. def logName: String

    Attributes
    protected
    Definition Classes
    Logging

  28. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  29. def logTrace(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  30. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  31. def logWarning(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

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

    Definition Classes
    AnyRef

  33. final def notify(): Unit

    Definition Classes
    AnyRef

  34. final def notifyAll(): Unit

    Definition Classes
    AnyRef

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

    Definition Classes
    BDGSparkCommand

  36. def run(sc: SparkContext): Unit

    Definition Classes
    View → BDGSparkCommand

  37. def run(): Unit

    Definition Classes
    BDGSparkCommand → Runnable

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

    Definition Classes
    AnyRef

  39. def toString(): String

    Definition Classes
    AnyRef → Any

  40. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from BDGSparkCommand[ViewArgs]

Inherited from Logging

Inherited from BDGCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

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