ReferencePosition

Value Members

1. final def !=(arg0: Any): Boolean

   

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2. final def ##(): Int

   

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3. final def ==(arg0: Any): Boolean

   

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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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13. def equals(arg0: Any): Boolean

    

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14. def finalize(): Unit

    

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

    

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16. def hashCode(): Int

    

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17. final def isInstanceOf[T0]: Boolean

    

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

    

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19. final def notify(): Unit

    

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20. final def notifyAll(): Unit

    

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21. implicit def orderingForOptionalPositions: OptionalPositionOrdering.type

    

22. implicit def orderingForPositions: PositionOrdering.type

    

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

    

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24. def toString(): String

    

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25. final def wait(): Unit

    

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

    

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

    

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