Coverage

Coverage record for CoverageDataset.

Contains Region indexed by reference name, start and end, as well as the average coverage at each base pair in that region.

referenceName: The chromosome that this coverage was observed on.
start: The start coordinate of the region where this coverage value was observed.
end: The end coordinate of the region where this coverage value was observed.
count: The average coverage across this region.
optSampleId: Option of sampleId for this Coverage record

Linear Supertypes

Serializable, Serializable, Product, Equals, AnyRef, Any

Instance Constructors

new Coverage(referenceName: String, start: Long, end: Long, count: Double, optSampleId: Option[String] = None)

referenceName
The chromosome that this coverage was observed on.
start
The start coordinate of the region where this coverage value was observed.
end
The end coordinate of the region where this coverage value was observed.
count
The average coverage across this region.
optSampleId
Option of sampleId for this Coverage record

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
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
val count: Double

The average coverage across this region.
val end: Long

The end coordinate of the region where this coverage value was observed.
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
final def isInstanceOf[T0]: Boolean

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

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val optSampleId: Option[String]

Option of sampleId for this Coverage record
val referenceName: String

The chromosome that this coverage was observed on.
val start: Long

The start coordinate of the region where this coverage value was observed.
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toFeature: Feature

Converts Coverage to Feature, setting Coverage count in the score attribute.
Converts Coverage to Feature, setting Coverage count in the score attribute.
returns
Feature built from Coverage
def toSqlFeature: Feature

Converts Coverage to a Feature case class, for use with Spark SQL.
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 Doc: package models

case class Coverage(referenceName: String, start: Long, end: Long, count: Double, optSampleId: Option[String] = None) extends Product with Serializable

Instance Constructors

new Coverage(referenceName: String, start: Long, end: Long, count: Double, optSampleId: Option[String] = None)

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def clone(): AnyRef

val count: Double

val end: Long

final def eq(arg0: AnyRef): Boolean

def finalize(): Unit

final def getClass(): Class[_]

final def isInstanceOf[T0]: Boolean

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val optSampleId: Option[String]

val referenceName: String

val start: Long

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

def toFeature: Feature

def toSqlFeature: Feature

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 AnyRef

Inherited from Any

Ungrouped