org.bdgenomics.adam.models

# ReferenceRegion

#### object ReferenceRegion extends Serializable

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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. #### def apply(feature: Feature): ReferenceRegion

5. #### def apply(fragment: NucleotideContigFragment): Option[ReferenceRegion]

   Generates a reference region from assembly data.

   Generates a reference region from assembly data. Returns None if the assembly does not have an ID or a start position.

   fragment

     Assembly fragment from which to generate data.

   returns

     Region corresponding to inclusive region of contig fragment.

6. #### def apply(pos: ReferencePosition): ReferenceRegion

   Generates a region from a given position -- the region will have a length of 1.

   Generates a region from a given position -- the region will have a length of 1.

   pos

     The position to convert

   returns

     A 1-wide region at the same location as pos

7. #### def apply(record: AlignmentRecord): ReferenceRegion

8. #### final def asInstanceOf[T0]: T0

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9. #### def clone(): AnyRef

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10. #### final def eq(arg0: AnyRef): Boolean

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11. #### def equals(arg0: Any): Boolean

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12. #### def finalize(): Unit

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

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17. #### final def notify(): Unit

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18. #### final def notifyAll(): Unit

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19. #### def opt(record: AlignmentRecord): Option[ReferenceRegion]

    Generates a reference region from read data.

    Generates a reference region from read data. Returns None if the read is not mapped; else, returns the inclusive region from the start to the end of the read alignment.

    record

      Read to create region from.

    returns

      Region corresponding to inclusive region of read alignment, if read is mapped.

20. #### implicit def orderingForOptionalPositions: OptionalRegionOrdering.type

21. #### implicit def orderingForPositions: RegionOrdering.type

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

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23. #### def toString(): String

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24. #### final def wait(): Unit

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

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26. #### final def wait(arg0: Long): Unit

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