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

   Definition Classes

   AnyRef

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

   Definition Classes

   Any

6. def apply(locus: Locus): Byte

7. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

8. val bases: Bases

9. def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

10. def contains(locus: Locus): Boolean

    Definition Classes

    Interval

11. val contigName: ContigName

    Definition Classes

    Slice → HasContig

12. val end: Locus

    0-based end position on a contig.

    0-based end position on a contig.

    Definition Classes

    Slice → Interval

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

    Definition Classes

    AnyRef

14. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

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

    Definition Classes

    AnyRef → Any

16. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

17. def iterator(): Iterator[Locus]

    Iterate through elements in the range.

    Iterate through elements in the range.

    Definition Classes

    Interval

18. def length: NumLoci

    Number of elements in the range.

    Number of elements in the range.

    Definition Classes

    Interval

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

    Definition Classes

    AnyRef

20. final def notify(): Unit

    Definition Classes

    AnyRef

21. final def notifyAll(): Unit

    Definition Classes

    AnyRef

22. def overlaps(other: Region): 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

    Region

23. def overlapsLocus(locus: Locus, halfWindowSize: WindowSize = 0): Boolean

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

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

    Definition Classes

    Region

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

25. val start: Locus

    0-based start position on a contig.

    0-based start position on a contig.

    Definition Classes

    Slice → Interval

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

    Definition Classes

    AnyRef

27. def toString(): String

    Definition Classes

    Region → Interval → Any

28. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )