PileupElement

Value Members

1. final def !=(arg0: AnyRef): Boolean

   Definition Classes

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2. final def !=(arg0: Any): Boolean

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3. final def ##(): Int

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4. final def ==(arg0: AnyRef): Boolean

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

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6. final def advanceToLocus(newLocus: Locus): PileupElement

   Returns a new PileupElement of the same read at a different locus.

   Returns a new PileupElement of the same read at a different locus.

   To enable an efficient implementation, newLocus must be greater than the current locus.

   newLocus

   The desired locus of the new PileupElement. It must be greater than the current locus, and not past the end of the current read.

   returns

   A new PileupElement at the given locus.

   Annotations

   @tailrec()

7. def advanceToNextCigarElement: PileupElement

   Returns a new PileupElement of the same read, advanced by one cigar element.

8. lazy val alignment: Alignment

9. lazy val allele: Allele

10. final def asInstanceOf[T0]: T0

    Definition Classes

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11. def cigarElement: CigarElement

12. def cigarElementEndLocus: Long

13. val cigarElementIndex: Int

    The index in the read's sequence of cigar elements (org.hammerlab.guacamole.reads.MappedRead.cigarElements) of the element that contains the current readPosition.

14. val cigarElementLocus: Locus

    The reference START position of the current cigar element.

    The reference START position of the current cigar element. If the element is an INSERTION this the PRECEDING reference base

15. def cigarElementReadLength: Int

16. def cigarElementReferenceLength: Int

17. def clone(): AnyRef

    Attributes

    protected[java.lang]

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    @throws( ... )

18. val contigSequence: ContigSequence

19. def currentCigarElementContainsLocus(referenceLocus: Locus): Boolean

    Returns whether the current cigar element of this org.hammerlab.guacamole.reads.MappedRead contains the given reference locus.

    Returns whether the current cigar element of this org.hammerlab.guacamole.reads.MappedRead contains the given reference locus.

    Can only return true if the cigar element consumes reference bases.

20. def distanceFromSequencingEnd: Long

    Distance from the end of the reading frame If the read was positive then the sequencing end also corresponds to the read end positions If the read was negative, the sequencing end is the mapped start position

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

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22. def finalize(): Unit

    Attributes

    protected[java.lang]

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

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

    Definition Classes

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24. val indexWithinCigarElement: Int

    The offset of this element within the current cigar element.

25. def isClipped: Boolean

26. def isDeletion: Boolean

27. def isFinalCigarBase: Boolean

28. def isInsertion: Boolean

29. final def isInstanceOf[T0]: Boolean

    Definition Classes

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30. def isMatch: Boolean

31. def isMidDeletion: Boolean

32. def isMismatch: Boolean

33. val locus: Locus

    The reference locus.

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

    Definition Classes

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35. def nextCigarElement: Option[CigarElement]

36. final def notify(): Unit

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37. final def notifyAll(): Unit

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38. def probabilityCorrectIgnoringAlignment: Double

39. def probabilityCorrectIncludingAlignment: Double

40. def qualityScore: Int

41. val read: MappedRead

    The read this PileupElement is coming from.

42. val readPosition: Int

    The offset into the sequence of bases in the read that this element corresponds to.

43. val referenceBase: Byte

44. def referenceBases: Seq[Byte]

45. def referenceStringIndex: Int

46. def sequencedBases: Seq[Byte]

    The sequenced nucleotides at this element.

    The sequenced nucleotides at this element.

    If the current element is a deletion, then this is the empty array. If it's an insertion, then this will be an array of length >= 1: the contents of the inserted sequence starting at the current locus. Otherwise, this is an array of length 1.

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

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48. final def wait(): Unit

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    @throws( ... )

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

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    @throws( ... )

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

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    @throws( ... )