RichAlignmentRecord

Value Members

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 finalize(): Unit

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10. def fivePrimePosition: Long

    returns

    The position of the five prime end of the read.

11. def fivePrimeReferencePosition: ReferencePosition

    returns

    The position of the five prime end of the read, wrapped as a reference position.

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

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13. final def isInstanceOf[T0]: Boolean

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14. def isMismatchAtReferencePosition(pos: ReferencePosition): Option[Boolean]

    pos

    The reference position to check for a mismatch.

    returns

    Returns true if this read overlaps the given reference position, and the base aligned at this position is a mismatch against the reference genome..

15. lazy val mdTag: Option[MdTag]

    The MdTag if the read is mapped, None otherwise

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

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17. final def notify(): Unit

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18. final def notifyAll(): Unit

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19. def overlapsReferencePosition(pos: ReferencePosition): Boolean

    pos

    The reference position to check for overlap.

    returns

    Returns true if this read overlaps the given reference position.

20. lazy val qualityScores: Array[Int]

    The quality scores as a list of integers.

    The quality scores as a list of integers. Assumes Illumina (33) encoding.

21. val record: AlignmentRecord

    The underlying read.

22. lazy val samtoolsCigar: Cigar

    Parses the text CIGAR representation of the alignment.

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

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24. lazy val tags: Seq[Attribute]

    On access, parses the attribute tags ("key:type:value" triples) into usable records.

25. lazy val unclippedEnd: Long

    The position of the unclipped end if the read is mapped, None otherwise.

    The position of the unclipped end if the read is mapped, None otherwise.

    Note

    The unclipped position assumes that any clipped bases would've been aligned as an alignment match.

26. lazy val unclippedStart: Long

    The position of the unclipped start if the read is mapped, None otherwise.

    The position of the unclipped start if the read is mapped, None otherwise.

    Note

    The unclipped position assumes that any clipped bases would've been aligned as an alignment match.

27. final def wait(): Unit

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

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

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