object ReferencePosition extends Serializable

Companion object for creating and sorting ReferencePositions.

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  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
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  4. 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.g.

    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).

  5. def apply(referenceName: String, pos: Long, strand: Strand): ReferencePosition

    Convenience method for building a ReferencePosition.

    Convenience method for building a ReferencePosition.

    referenceName

    The name of the reference sequence this locus exists on.

    pos

    The position of this locus.

    strand

    The strand that this locus is on.

  6. 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 sequence this locus exists on.

    pos

    The position of this locus.

  7. 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.

  8. 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.

  9. def apply(record: Alignment): 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

  10. final def asInstanceOf[T0]: T0
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  11. def clone(): AnyRef
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  12. final def eq(arg0: AnyRef): Boolean
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  19. final def notifyAll(): Unit
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  20. implicit def orderingForOptionalPositions: OptionalPositionOrdering.type
  21. implicit def orderingForPositions: PositionOrdering.type
  22. final def synchronized[T0](arg0: ⇒ T0): T0
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  1. def finalize(): Unit
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    Deprecated

    (Since version ) see corresponding Javadoc for more information.

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