ReferencePositionWithOrientation

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. def apply(record: AlignmentRecord): Option[ReferencePositionWithOrientation]

7. final def asInstanceOf[T0]: T0

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8. def clone(): AnyRef

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

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10. def equals(arg0: Any): Boolean

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11. def finalize(): Unit

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12. def fivePrime(record: AlignmentRecord): Option[ReferencePositionWithOrientation]

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

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14. def hashCode(): Int

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15. final def isInstanceOf[T0]: Boolean

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16. def liftOverToReference(idx: Long, mapping: Seq[ReferenceRegionWithOrientation]): ReferencePositionWithOrientation

    Given an index into a sequence (e.

    Given an index into a sequence (e.g., a transcript), and a sequence of regions that map this sequence to a reference genome, returns a reference position.

    idx

    Index into a sequence.

    mapping

    Sequence of reference regions that maps the sequence to a reference genome.

    returns

    Returns a lifted over reference position.

    Exceptions thrown

    AssertionError

    Throws an assertion error if the strandedness does not match between the reference position and the mapping regions.

    IllegalArgumentException

    Throws an exception if the index given is out of the range of the mappings given.

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

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18. final def notify(): Unit

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19. final def notifyAll(): Unit

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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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