ReadBucket

This class is similar to SingleReadBucket, except it breaks the reads down further.

Rather than stopping at primary/secondary/unmapped, this will break it down further into whether they are paired or unpaired, and then whether they are the first or second of the pair.

This is useful as this will usually map a single read in any of the sequences.

Linear Supertypes

Serializable, Serializable, Product, Equals, AnyRef, Any

Instance Constructors

new ReadBucket(unpairedPrimaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, pairedFirstPrimaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, pairedSecondPrimaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, unpairedSecondaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, pairedFirstSecondaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, pairedSecondSecondaryMappedReads: Iterable[AlignmentRecord] = Seq.empty, unmappedReads: Iterable[AlignmentRecord] = Seq.empty)

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 allReads(): Iterable[AlignmentRecord]
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
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 pairedFirstPrimaryMappedReads: Iterable[AlignmentRecord]
val pairedFirstSecondaryMappedReads: Iterable[AlignmentRecord]
val pairedSecondPrimaryMappedReads: Iterable[AlignmentRecord]
val pairedSecondSecondaryMappedReads: Iterable[AlignmentRecord]
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
val unmappedReads: Iterable[AlignmentRecord]
val unpairedPrimaryMappedReads: Iterable[AlignmentRecord]
val unpairedSecondaryMappedReads: Iterable[AlignmentRecord]
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 ReadBucket | package models

Instance Constructors

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

def allReads(): Iterable[AlignmentRecord]

final def asInstanceOf[T0]: T0

def clone(): AnyRef

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 pairedFirstPrimaryMappedReads: Iterable[AlignmentRecord]

val pairedFirstSecondaryMappedReads: Iterable[AlignmentRecord]

val pairedSecondPrimaryMappedReads: Iterable[AlignmentRecord]

val pairedSecondSecondaryMappedReads: Iterable[AlignmentRecord]

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

val unmappedReads: Iterable[AlignmentRecord]

val unpairedPrimaryMappedReads: Iterable[AlignmentRecord]

val unpairedSecondaryMappedReads: Iterable[AlignmentRecord]

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