ReadGroup

A read group represents a set of reads that were sequenced/processed/prepped/analyzed together.

sampleId: The sample these reads are from.
id: The identifier for this read group.
sequencingCenter: The optional name of the place where these reads were sequenced.
description: An optional description for this read group.
runDateEpoch: An optional Unix epoch timestamp for when these reads were run through the sequencer.
flowOrder: An optional string of nucleotides that were used for each flow of each read.
keySequence: An optional string of nucleotides that are the key for this read.
library: An optional library name.
predictedMedianInsertSize: An optional prediction of the read insert size for this library prep.
platform: An optional description for the platform this group was sequenced on.
platformUnit: An optional ID for the sequencer this group was sequenced on.

Linear Supertypes

Serializable, Serializable, Product, Equals, AnyRef, Any

Instance Constructors

new ReadGroup(sampleId: String, id: String, sequencingCenter: Option[String] = None, description: Option[String] = None, runDateEpoch: Option[Long] = None, flowOrder: Option[String] = None, keySequence: Option[String] = None, library: Option[String] = None, predictedMedianInsertSize: Option[Int] = None, platform: Option[String] = None, platformUnit: Option[String] = None)

sampleId
The sample these reads are from.
id
The identifier for this read group.
sequencingCenter
The optional name of the place where these reads were sequenced.
description
An optional description for this read group.
runDateEpoch
An optional Unix epoch timestamp for when these reads were run through the sequencer.
flowOrder
An optional string of nucleotides that were used for each flow of each read.
keySequence
An optional string of nucleotides that are the key for this read.
library
An optional library name.
predictedMedianInsertSize
An optional prediction of the read insert size for this library prep.
platform
An optional description for the platform this group was sequenced on.
platformUnit
An optional ID for the sequencer this group was sequenced on.

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 description: Option[String]

An optional description for this read group.
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def equals(o: Any): Boolean

Compares equality to another object.
Compares equality to another object. Only checks equality via the sampleId and id fields.
o
Object to compare against.
returns
Returns true if the object is a ReadGroup, and the sampleId and id fields are equal. Else, returns false.

Definition Classes
ReadGroup → Equals → AnyRef → Any
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
val flowOrder: Option[String]

An optional string of nucleotides that were used for each flow of each read.
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def hashCode(): Int

Generates a hash from the sampleId and id fields.
Generates a hash from the sampleId and id fields.
returns
Hash code for this object.

Definition Classes
ReadGroup → AnyRef → Any
val id: String

The identifier for this read group.
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
val keySequence: Option[String]

An optional string of nucleotides that are the key for this read.
val library: Option[String]

An optional library name.
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val platform: Option[String]

An optional description for the platform this group was sequenced on.
val platformUnit: Option[String]

An optional ID for the sequencer this group was sequenced on.
val predictedMedianInsertSize: Option[Int]

An optional prediction of the read insert size for this library prep.
val runDateEpoch: Option[Long]

An optional Unix epoch timestamp for when these reads were run through the sequencer.
val sampleId: String

The sample these reads are from.
val sequencingCenter: Option[String]

The optional name of the place where these reads were sequenced.
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toMetadata: formats.avro.ReadGroup

Converts this into an Avro ReadGroup description for serialization to disk.
Converts this into an Avro ReadGroup description for serialization to disk.
returns
Returns Avro version of ReadGroup.
def toSAMReadGroupRecord(): SAMReadGroupRecord

Converts a read group into a SAM formatted read group.
Converts a read group into a SAM formatted read group.
returns
A SAM formatted read group.
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 ReadGroup | package models

Instance Constructors

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def clone(): AnyRef

val description: Option[String]

final def eq(arg0: AnyRef): Boolean

def equals(o: Any): Boolean

def finalize(): Unit

val flowOrder: Option[String]

final def getClass(): Class[_]

def hashCode(): Int

val id: String

final def isInstanceOf[T0]: Boolean

val keySequence: Option[String]

val library: Option[String]

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val platform: Option[String]

val platformUnit: Option[String]

val predictedMedianInsertSize: Option[Int]

val runDateEpoch: Option[Long]

val sampleId: String

val sequencingCenter: Option[String]

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

def toMetadata: formats.avro.ReadGroup

def toSAMReadGroupRecord(): SAMReadGroupRecord

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