Slice

Value Members

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

   Definition Classes

   AnyRef

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

   Definition Classes

   Any

3. final def ##(): Int

   Definition Classes

   AnyRef → Any

4. def <(that: Interval): Boolean

   Definition Classes

   Ordered

5. def <=(that: Interval): Boolean

   Definition Classes

   Ordered

6. final def ==(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

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

   Definition Classes

   Any

8. def >(that: Interval): Boolean

   Definition Classes

   Ordered

9. def >=(that: Interval): Boolean

   Definition Classes

   Ordered

10. def apply(locus: Locus): Byte

11. final def asInstanceOf[T0]: T0

    Definition Classes

    Any

12. val bases: Seq[Byte]

13. def clone(): AnyRef

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

14. def compare(other: Interval): Int

    Comparisons between ranges.

    Comparisons between ranges. Order is DESCENDING (i.e. reversed) from by start.

    Definition Classes

    Interval → Ordered

15. def compareTo(that: Interval): Int

    Definition Classes

    Ordered → Comparable

16. def contains(locus: Locus): Boolean

    Definition Classes

    Interval

17. val contigName: ContigName

    Name of the reference contig.

    Name of the reference contig.

    Definition Classes

    Slice → ReferenceRegion → HasContig

18. val end: Locus

    The end position on the genome, *exclusive*.

    The end position on the genome, *exclusive*. Must be non-negative.

    Definition Classes

    Slice → Interval

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

    Definition Classes

    AnyRef

20. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

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

    Definition Classes

    AnyRef → Any

22. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

23. def iterator(): Iterator[Long]

    Iterate through elements in the range.

    Iterate through elements in the range.

    Definition Classes

    Interval

24. def length: NumLoci

    Number of elements in the range.

    Number of elements in the range.

    Definition Classes

    Interval

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

    Definition Classes

    AnyRef

26. final def notify(): Unit

    Definition Classes

    AnyRef

27. final def notifyAll(): Unit

    Definition Classes

    AnyRef

28. def overlaps(other: ReferenceRegion): Boolean

    Does the region overlap another reference region

    Does the region overlap another reference region

    other

    another region on the genome

    returns

    True if the the regions overlap

    Definition Classes

    ReferenceRegion

29. def overlapsLocus(locus: Locus, halfWindowSize: Int = 0): Boolean

    Does the region overlap the given locus, with halfWindowSize padding?

    Does the region overlap the given locus, with halfWindowSize padding?

    Definition Classes

    ReferenceRegion

30. def regionStr: String

    Definition Classes

    ReferenceRegion

31. def slice(sliceStart: Locus, sliceEnd: Locus = end): Seq[Byte]

32. val start: Locus

    Start position on the genome, inclusive.

    Start position on the genome, inclusive. Must be non-negative.

    Definition Classes

    Slice → Interval

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

    Definition Classes

    AnyRef

34. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )