LociSet

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.

Linear Supertypes

Serializable, Serializable, Product, Equals, TruncatedToString, AnyRef, Any

Instance Constructors

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

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

Definition Classes
AnyRef → Any
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def apply(contigName: ContigName): Contig

Given a contig name, returns a Contig giving the loci on that contig.
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
lazy val contigs: Array[Contig]

The contigs included in this LociSet with a nonempty set of loci.
lazy val count: NumLoci

The number of loci in this LociSet.
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def intersects(region: Region): Boolean
def isEmpty: Boolean
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def nonEmpty: Boolean
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
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
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
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.
def toHtsJDKIntervals: List[Interval]

Build a collection of HTSJDK Intervals which are closed [start, end], 1-based intervals
def toString(maxLength: Int, separator: String, ellipses: String): String

Definition Classes
TruncatedToString
def toString(): String

Definition Classes
TruncatedToString → AnyRef → Any
final def wait(): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long, arg1: Int): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )

Related Docs: object LociSet | package set

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

Instance Constructors

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

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

def apply(contigName: ContigName): Contig

final def asInstanceOf[T0]: T0

def clone(): AnyRef

lazy val contigs: Array[Contig]

lazy val count: NumLoci

final def eq(arg0: AnyRef): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def intersects(region: Region): Boolean

def isEmpty: Boolean

final def isInstanceOf[T0]: Boolean

final def ne(arg0: AnyRef): Boolean

def nonEmpty: Boolean

final def notify(): Unit

final def notifyAll(): Unit

def stringPieces: Iterator[String]

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

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

def toHtsJDKIntervals: List[Interval]

def toString(maxLength: Int, separator: String, ellipses: String): String

def toString(): String

final def wait(): Unit

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

final def wait(arg0: Long): Unit

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from TruncatedToString

Inherited from AnyRef

Inherited from Any

Ungrouped