ReadSubsequence

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

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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 asInstanceOf[T0]: T0

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7. def clone(): AnyRef

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

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9. def equals(arg0: Any): Boolean

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10. def finalize(): Unit

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

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12. def hashCode(): Int

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13. final def isInstanceOf[T0]: Boolean

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

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15. def nextAlts(elements: Seq[PileupElement]): Seq[ReadSubsequence]

    Given any number of pileup elements, return all alternate alleles starting at the elements' locus + 1.

    Given any number of pileup elements, return all alternate alleles starting at the elements' locus + 1.

    elements

    pileup element instances, should all be positioned at same locus

    returns

    ReadSubsequence instances giving the non-reference sequenced alleles at this position

16. final def notify(): Unit

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17. final def notifyAll(): Unit

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18. def ofFixedReferenceLength(element: PileupElement, length: Int): Option[ReadSubsequence]

    Extract a sub-sequence of a particular length starting at a certain reference locus from a MappedRead.

    Extract a sub-sequence of a particular length starting at a certain reference locus from a MappedRead.

    element

    PileupElement positioned at one reference base before the start of the desired sub-sequence

    length

    reference length of the desired ReadSubsequence.

    returns

    The sub-sequence of sequenced bases from element.read starting at reference position element.locus + 1 and spanning reference length refSequence.length. If the base aligning to element.locus is non-reference base, or the read ends before the end of the reference region, the result is None.

19. def ofNextAltAllele(element: PileupElement): Option[ReadSubsequence]

    Extract a sub-sequence containing an alternate allele, if there is one, from a PileupElement's subsequent position.

    Extract a sub-sequence containing an alternate allele, if there is one, from a PileupElement's subsequent position.

    If the element is currently NOT positioned at an alt, but the *following* base is an alt, then return a ReadSubsequence comprising the consecutive alternate sequenced bases, which could be any length. If the element's current position is at a non-reference-matching base, or the subsequent bases match the reference, or the read ends before a reference-matching base occurs, then return None.

    element

    PileupElement positioned at one reference base before the start of the desired sub-sequence

    returns

    ReadSubsequence for the alt allele, if one exists

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

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21. def toString(): String

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22. final def wait(): Unit

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

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

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