TransformAlignments

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

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

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   Any

6. def apply(rdd: AlignmentRecordRDD): AlignmentRecordRDD

7. val args: TransformAlignmentsArgs

   Attributes

   protected

   Definition Classes

   TransformAlignments → BDGSparkCommand

8. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

9. def clone(): AnyRef

   Attributes

   protected[java.lang]

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   Annotations

   @throws( ... )

10. val companion: TransformAlignments.type

    Definition Classes

    TransformAlignments → 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]

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    Annotations

    @throws( classOf[java.lang.Throwable] )

14. def forceNonParquet(): Boolean

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

    Definition Classes

    AnyRef → Any

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 isNonParquet(inputPath: String): Boolean

20. def isTraceEnabled(): Boolean

    Attributes

    protected

    Definition Classes

    Logging

21. def log: Logger

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    protected

    Definition Classes

    Logging

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

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    Definition Classes

    Logging

23. def logDebug(msg: ⇒ String): Unit

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    protected

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    Logging

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

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    Logging

25. def logError(msg: ⇒ String): Unit

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    Logging

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

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    Logging

27. def logInfo(msg: ⇒ String): Unit

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    Logging

28. def logName: String

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    Logging

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

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    protected

    Definition Classes

    Logging

30. def logTrace(msg: ⇒ String): Unit

    Attributes

    protected

    Definition Classes

    Logging

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

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    protected

    Definition Classes

    Logging

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

    Attributes

    protected

    Definition Classes

    Logging

33. def maybeMdTag(sc: SparkContext, rdd: AlignmentRecordRDD, stringencyOpt: Option[ValidationStringency]): AlignmentRecordRDD

    rdd

    The RDD of reads that was output by maybeSort.

    stringencyOpt

    An optional validation stringency.

    returns

    If -add_md_tags is set, recomputes the MD tags for the reads provided. If some reads have tags, -md_tag_overwrite controls whether these tags are recomputed or not. If MD tagging isn't requested, we return the input RDD.

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

    Definition Classes

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35. final def notify(): Unit

    Definition Classes

    AnyRef

36. final def notifyAll(): Unit

    Definition Classes

    AnyRef

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

    Definition Classes

    BDGSparkCommand

38. def run(sc: SparkContext): Unit

    Definition Classes

    TransformAlignments → BDGSparkCommand

39. def run(): Unit

    Definition Classes

    BDGSparkCommand → Runnable

40. val stringency: ValidationStringency

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

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    AnyRef

42. def toString(): String

    Definition Classes

    AnyRef → Any

43. final def wait(): Unit

    Definition Classes

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    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )