org.bdgenomics.adam.cli

# TransformAlignments

###
Related Docs: object TransformAlignments | package cli

#### class TransformAlignments extends BDGSparkCommand[TransformAlignmentsArgs] with Logging

Linear Supertypes
BDGSparkCommand[TransformAlignmentsArgs], Logging, BDGCommand, Runnable, AnyRef, Any
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Inherited

1. TransformAlignments
2. BDGSparkCommand
3. Logging
4. BDGCommand
5. Runnable
6. AnyRef
7. Any

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Visibility

1. Public
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### Instance Constructors

1. #### new TransformAlignments(args: TransformAlignmentsArgs)

### 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 apply(rdd: AlignmentRecordRDD): AlignmentRecordRDD

5. #### val args: TransformAlignmentsArgs

   Attributes
     protected
   Definition Classes
     TransformAlignments → 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: TransformAlignments.type

   Definition Classes
     TransformAlignments → 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. #### def forceNonParquet(): Boolean

13. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

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 isNonParquet(inputPath: String): Boolean

18. #### def isTraceEnabled(): Boolean

    Attributes
      protected
    Definition Classes
      Logging

19. #### def log: Logger

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

21. #### def logDebug(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

23. #### def logError(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

25. #### def logInfo(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

26. #### def logName: String

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

28. #### def logTrace(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

30. #### def logWarning(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

31. #### 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.

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
      TransformAlignments → BDGSparkCommand

37. #### def run(): Unit

    Definition Classes
      BDGSparkCommand → Runnable

38. #### val stringency: ValidationStringency

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

    Definition Classes
      AnyRef

40. #### def toString(): String

    Definition Classes
      AnyRef → Any

41. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

43. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from BDGSparkCommand[TransformAlignmentsArgs]

### Inherited from Logging

### Inherited from BDGCommand

### Inherited from Runnable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped