ReferenceRegion

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. def apply(coverage: Coverage): ReferenceRegion

   Builds a reference region for a coverage site.

   Builds a reference region for a coverage site.

   coverage

   Coverage to extract ReferenceRegion from

   returns

   Extracted ReferenceRegion

7. def apply(feature: Feature): ReferenceRegion

   Builds a reference region for a feature.

   Builds a reference region for a feature.

   feature

   Feature to extract ReferenceRegion from

   returns

   Extracted ReferenceRegion

8. 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.

9. 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

10. def apply(record: AlignmentRecord): ReferenceRegion

11. def apply(annotation: DatabaseVariantAnnotation): ReferenceRegion

12. def apply(variant: Variant): ReferenceRegion

    Builds a reference region for a variant site.

    Builds a reference region for a variant site.

    variant

    Variant to extract region from.

    returns

    The site where this variant covers.

13. def apply(genotype: Genotype): ReferenceRegion

    Builds a reference region for a called genotype.

    Builds a reference region for a called genotype.

    genotype

    Called genotype to extract region from.

    returns

    The site where this genotype lives.

14. final def asInstanceOf[T0]: T0

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15. def clone(): AnyRef

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

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17. def equals(arg0: Any): Boolean

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18. def finalize(): Unit

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

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20. def hashCode(): Int

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21. final def isInstanceOf[T0]: Boolean

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

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23. final def notify(): Unit

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24. final def notifyAll(): Unit

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25. 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.

26. implicit def orderingForOptionalPositions: OptionalRegionOrdering.type

27. implicit def orderingForPositions: RegionOrdering.type

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

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29. def toString(): String

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30. final def wait(): Unit

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

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

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