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
Ordering
  1. Alphabetic
  2. By Inheritance
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)

Type Members

  1. type ReadFilter = (AlignmentRecord) ⇒ Boolean

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. def applyFilters(reads: RDD[AlignmentRecord]): RDD[AlignmentRecord]
  5. val args: ViewArgs
    Definition Classes
    View → BDGSparkCommand
  6. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  7. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  8. val companion: View.type
    Definition Classes
    View → BDGCommand
  9. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  10. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  11. def debug(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  12. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  13. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  14. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  15. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  16. def error(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  17. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  18. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  19. def getFilters(n: Int, matchValue: Boolean = true): List[ReadFilter]
  20. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  21. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  22. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  23. def info(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  24. def initializeMetrics(sc: SparkContext): Option[MetricsListener]
    Definition Classes
    BDGSparkCommand
  25. def isDebugEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  26. def isErrorEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  27. def isInfoEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  28. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  29. def isTraceEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  30. def isWarnEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  31. def logger: Logger
    Attributes
    protected
    Definition Classes
    Logging
  32. def loggerName: String
    Attributes
    protected
    Definition Classes
    Logging
  33. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  34. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  35. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  36. def printMetrics(totalTime: Long, metricsListener: Option[MetricsListener]): Unit
    Definition Classes
    BDGSparkCommand
  37. def run(sc: SparkContext): Unit
    Definition Classes
    View → BDGSparkCommand
  38. def run(): Unit
    Definition Classes
    BDGSparkCommand → Runnable
  39. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  40. def toString(): String
    Definition Classes
    AnyRef → Any
  41. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  42. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  43. def trace(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  44. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  45. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  46. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  47. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  48. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  49. def warn(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging

Inherited from BDGSparkCommand[ViewArgs]

Inherited from Logging

Inherited from BDGCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

Ungrouped