DeBruijnGraph

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

   Definition Classes

   AnyRef

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

   Definition Classes

   Any

6. def apply(reads: Seq[Read], kmerSize: Int, minOccurrence: Int = 1, minMeanKmerBaseQuality: Int = 0, mergeNodes: Boolean = false): DeBruijnGraph

7. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

8. def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

9. def discoverPathsFromReads(reads: Seq[MappedRead], referenceStart: Int, referenceEnd: Int, referenceSequence: Array[Byte], kmerSize: Int, minOccurrence: Int, maxPaths: Int, minMeanKmerBaseQuality: Int, debugPrint: Boolean = false): List[List[Seq[Byte]]]

   Find paths through the reads given that represent the sequence covering referenceStart and referenceEnd

   Find paths through the reads given that represent the sequence covering referenceStart and referenceEnd

   reads

   Reads to use to build the graph

   referenceStart

   Start of the reference region corresponding to the reads

   referenceEnd

   End of the reference region corresponding to the reads

   referenceSequence

   Reference sequence overlapping [referenceStart, referenceEnd)

   kmerSize

   Length of kmers to use to traverse the paths

   minOccurrence

   Minimum number of occurrences of the each kmer

   maxPaths

   Maximum number of paths to find

   debugPrint

   Print debug statements (default: false)

   returns

   List of paths that traverse the region

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

    Definition Classes

    AnyRef

11. def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

12. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

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

    Definition Classes

    AnyRef → Any

14. def hashCode(): Int

    Definition Classes

    AnyRef → Any

15. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

16. def mergeOverlappingSequences(sequences: Seq[Sequence], overlapSize: Int): Sequence

    Merge sequences where we expect consecutive entries to overlap by overlapSize bases.

    Merge sequences where we expect consecutive entries to overlap by overlapSize bases.

    sequences

    Set of sequences that we would like to combine into a single sequence

    overlapSize

    The amount of the sequences we expect to overlap (The number of bases the last sequence overlaps with the next. For a standard kmer graph, this is the length of the kmer length - 1

    returns

    A single merged sequence

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

    Definition Classes

    AnyRef

18. final def notify(): Unit

    Definition Classes

    AnyRef

19. final def notifyAll(): Unit

    Definition Classes

    AnyRef

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

    Definition Classes

    AnyRef

21. def toString(): String

    Definition Classes

    AnyRef → Any

22. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )