ConsensusGeneratorFromReads

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. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

5. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

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

   

   Definition Classes

   AnyRef

7. def equals(arg0: Any): Boolean

   

   Definition Classes

   AnyRef → Any

8. def finalize(): Unit

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

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

9. def findConsensus(reads: Iterable[RichAlignmentRecord]): Iterable[Consensus]

   

   Generates concensus sequences from reads with indels.

   Generates concensus sequences from reads with indels.

   reads

   Reads to generate consensus sequences from.

   returns

   Consensus sequences to use for realignment.

   Definition Classes

   ConsensusGeneratorFromReads → ConsensusGenerator

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

    

    Definition Classes

    AnyRef → Any

11. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

12. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

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

    

    Definition Classes

    AnyRef

14. final def notify(): Unit

    

    Definition Classes

    AnyRef

15. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

16. def preprocessReadsForRealignment(reads: Iterable[RichAlignmentRecord], reference: String, region: ReferenceRegion): Iterable[RichAlignmentRecord]

    

    Performs read preprocessing by normalizing indels for all reads that have evidence of one indel.

    Performs read preprocessing by normalizing indels for all reads that have evidence of one indel.

    reads

    Reads to process.

    returns

    Reads with indels normalized if they contain a single indel.

    Definition Classes

    ConsensusGeneratorFromReads → ConsensusGenerator

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

    

    Definition Classes

    AnyRef

18. def targetsToAdd(): Option[RDD[IndelRealignmentTarget]]

    

    No targets to add if generating consensus targets from reads.

    No targets to add if generating consensus targets from reads.

    returns

    Returns a None.

    Definition Classes

    ConsensusGeneratorFromReads → ConsensusGenerator

19. def toString(): String

    

    Definition Classes

    AnyRef → Any

20. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )