org.hammerlab.guacamole.loci.set

LociSet

case class LociSet(map: SortedMap[ContigName, Contig]) extends TruncatedToString with Product with Serializable

An immutable collection of genomic regions on any number of contigs.

Used, for example, to keep track of what loci to call variants at.

Since contiguous genomic intervals are a common case, this is implemented with sets of (start, end) intervals.

All intervals are half open: inclusive on start, exclusive on end.

map

A map from contig-name to Contig, which is a set or genomic intervals as described above.

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Serializable, Serializable, Product, Equals, TruncatedToString, AnyRef, Any
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Instance Constructors

  1. new LociSet(map: SortedMap[ContigName, Contig])

    map

    A map from contig-name to Contig, which is a set or genomic intervals as described above.

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. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  8. lazy val contigs: Array[Contig]

    The contigs included in this LociSet with a nonempty set of loci.

  9. lazy val count: NumLoci

    The number of loci in this LociSet.

  10. def difference(other: LociSet): LociSet

    Intersect this LociSet with another

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

    Definition Classes
    AnyRef

  12. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

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

    Definition Classes
    AnyRef → Any

  14. def intersect(other: LociSet): LociSet

    Intersect this LociSet with another

  15. def intersects(region: ReferenceRegion): Boolean

  16. def isEmpty: Boolean

  17. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  19. def nonEmpty: Boolean

  20. final def notify(): Unit

    Definition Classes
    AnyRef

  21. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  22. def onContig(name: ContigName): Contig

    Given a contig name, returns a Contig giving the loci on that contig.

  23. def stringPieces: Iterator[String]

    Build a truncate-able toString() out of underlying contig pieces.

    Build a truncate-able toString() out of underlying contig pieces.

    Definition Classes
    LociSet → TruncatedToString

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

    Definition Classes
    AnyRef

  25. def take(numToTake: NumLoci): (LociSet, LociSet)

    Split the LociSet into two sets, where the first one has numToTake loci, and the second one has the remaining loci.

    Split the LociSet into two sets, where the first one has numToTake loci, and the second one has the remaining loci.

    numToTake

    number of elements to take. Must be <= number of elements in the map.

  26. def toHtsJDKIntervals: List[Interval]

    Build a collection of HTSJDK Intervals which are closed [start, end], 1-based intervals

  27. def toString(): String

    Definition Classes
    TruncatedToString → AnyRef → Any

  28. def truncatedString(maxLength: Int = 500): String

    String representation, truncated to maxLength characters.

    String representation, truncated to maxLength characters.

    Definition Classes
    TruncatedToString

  29. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from TruncatedToString

Inherited from AnyRef

Inherited from Any

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