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
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. View
  2. BDGSparkCommand
  3. Logging
  4. BDGCommand
  5. Runnable
  6. AnyRef
  7. Any
  1. Hide All
  2. Show all
Learn more about member selection
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
    @throws( ... )

  8. val companion: View.type

    Definition Classes
    View → BDGCommand

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

    Definition Classes
    AnyRef

  10. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  11. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

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

  14. def hashCode(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    BDGSparkCommand

  16. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  17. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging

  18. def log: Logger

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

  25. def logName: String

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Definition Classes
    AnyRef

  31. final def notify(): Unit

    Definition Classes
    AnyRef

  32. final def notifyAll(): Unit

    Definition Classes
    AnyRef

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

    Definition Classes
    BDGSparkCommand

  34. def run(sc: SparkContext): Unit

    Definition Classes
    View → BDGSparkCommand

  35. def run(): Unit

    Definition Classes
    BDGSparkCommand → Runnable

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

    Definition Classes
    AnyRef

  37. def toString(): String

    Definition Classes
    AnyRef → Any

  38. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  40. 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

Ungrouped