ReadGroupDictionary

Instance Constructors

new ReadGroupDictionary(readGroups: Seq[ReadGroup])

readGroups
A seq of read groups to populate the dictionary.

Exceptions thrown
IllegalArgumentException Throws an assertion error if there are multiple read groups with the same name.

Value Members

final def !=(arg0: Any): Boolean

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

Definition Classes
AnyRef → Any
def ++(that: ReadGroupDictionary): ReadGroupDictionary

Merges together two read group dictionaries.
Merges together two read group dictionaries.
that
The read group dictionary to merge with.
returns
The merged read group dictionary.
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def apply(readGroupId: String): ReadGroup

Returns the read group entry for an associated id.
Returns the read group entry for an associated id.
readGroupId
The read group to look up.
returns
Detailed info for a read group.
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
def getIndex(readGroupId: String): Int

Returns the numerical index for a given read group id.
Returns the numerical index for a given read group id.
readGroupId
The read group to find an index for.
returns
Returns a numerical index for a read group.

Note
This index is only guaranteed to have the same value for a given read group id when the index is pulled from the same read group dictionary.
def isEmpty: Boolean

returns
Returns true if this dictionary contains no read groups.
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 readGroupMap: Map[String, (ReadGroup, Int)]

A representation of this read group dictionary that can be indexed into by read group id.
val readGroups: Seq[ReadGroup]

A seq of read groups to populate the dictionary.
def size: Int

The number of read groups in the dictionary.
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toSamples: Seq[Sample]

returns
Converts this read group dictionary to a set of samples.
def toString(): String

Definition Classes
ReadGroupDictionary → 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 ReadGroupDictionary | package models

case class ReadGroupDictionary(readGroups: Seq[ReadGroup]) extends Product with Serializable

Instance Constructors

new ReadGroupDictionary(readGroups: Seq[ReadGroup])

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

def ++(that: ReadGroupDictionary): ReadGroupDictionary

final def ==(arg0: Any): Boolean

def apply(readGroupId: String): ReadGroup

final def asInstanceOf[T0]: T0

def clone(): AnyRef

final def eq(arg0: AnyRef): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def getIndex(readGroupId: String): Int

def isEmpty: Boolean

final def isInstanceOf[T0]: Boolean

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val readGroupMap: Map[String, (ReadGroup, Int)]

val readGroups: Seq[ReadGroup]

def size: Int

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

def toSamples: Seq[Sample]

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 AnyRef

Inherited from Any

Ungrouped