ReferencePosition

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. val UNMAPPED: ReferencePosition

   The UNMAPPED value is a convenience value, which can be used to indicate a position which is not located anywhere along the reference sequences (see, e.

   The UNMAPPED value is a convenience value, which can be used to indicate a position which is not located anywhere along the reference sequences (see, e.g. its use in GenomicPositionPartitioner).

7. def apply(referenceName: String, pos: Long, orientation: Strand): ReferencePosition

   Convenience method for building a ReferencePosition.

   Convenience method for building a ReferencePosition.

   referenceName

   The name of the reference contig this locus exists on.

   pos

   The position of this locus.

   orientation

   The strand that this locus is on.

8. def apply(referenceName: String, pos: Long): ReferencePosition

   Convenience method for building a ReferencePosition.

   Convenience method for building a ReferencePosition.

   referenceName

   The name of the reference contig this locus exists on.

   pos

   The position of this locus.

9. def apply(genotype: Genotype): ReferencePosition

   Generates a reference position from a genotype.

   Generates a reference position from a genotype.

   genotype

   Genotype from which to generate a reference position.

   returns

   The reference position of this genotype.

10. def apply(variant: Variant): ReferencePosition

    Generates a reference position from a called variant.

    Generates a reference position from a called variant.

    variant

    Called variant from which to generate a reference position.

    returns

    The reference position of this variant.

11. def apply(record: AlignmentRecord): ReferencePosition

    Generates a reference position from a read.

    Generates a reference position from a read. This function generates the position from the start mapping position of the read.

    record

    Read from which to generate a reference position.

    returns

    Reference position of the start position.

    See also

    fivePrime

12. final def asInstanceOf[T0]: T0

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13. def clone(): AnyRef

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

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15. def equals(arg0: Any): Boolean

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16. def finalize(): Unit

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

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18. def hashCode(): Int

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19. final def isInstanceOf[T0]: Boolean

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

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21. final def notify(): Unit

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22. final def notifyAll(): Unit

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23. implicit def orderingForOptionalPositions: OptionalPositionOrdering.type

24. implicit def orderingForPositions: PositionOrdering.type

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

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26. def toString(): String

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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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