org.bdgenomics.adam.models

# ReferencePosition

#### object ReferencePosition extends Serializable

Companion object for creating and sorting ReferencePositions.

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

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2. #### final def !=(arg0: Any): Boolean

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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, strand: 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.

   strand

     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

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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

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