PairedRead

Instance Constructors

new PairedRead(read: T, isFirstInPair: Boolean, mateAlignmentProperties: Option[MateAlignmentProperties])

read
Unmapped or MappedRead base read
isFirstInPair
Whether the read is earlier that the the mate read
mateAlignmentProperties
Alignment location of the mate if it the mate is aligned

Value Members

final def !=(arg0: AnyRef): Boolean

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

Definition Classes
Any
final def ##(): Int

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

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

Definition Classes
Any
final def asInstanceOf[T0]: T0

Definition Classes
Any
def asMappedRead: Option[MappedRead]

Definition Classes
PairedRead → Read
val baseQualities: IndexedSeq[Byte]

The base qualities, phred scaled.
The base qualities, phred scaled. These are numbers, and are NOT character encoded.

Definition Classes
PairedRead → Read
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
val failedVendorQualityChecks: Boolean

Whether the read failed predefined vendor checks for quality
Whether the read failed predefined vendor checks for quality

Definition Classes
PairedRead → Read
def finalize(): Unit

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

Definition Classes
AnyRef → Any
val isDuplicate: Boolean

Is this read a duplicate of another?
Is this read a duplicate of another?

Definition Classes
PairedRead → Read
val isFirstInPair: Boolean

Whether the read is earlier that the the mate read
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
val isMapped: Boolean

Is this read mapped?
Is this read mapped?

Definition Classes
PairedRead → Read
val isMateMapped: Boolean
val isPaired: Boolean

Whether read is from a paired-end library
Whether read is from a paired-end library

Definition Classes
PairedRead → Read
val mateAlignmentProperties: Option[MateAlignmentProperties]

Alignment location of the mate if it the mate is aligned
val name: String

Definition Classes
PairedRead → Read
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val read: T

Unmapped or MappedRead base read
val sampleId: SampleId

Definition Classes
PairedRead → HasSampleId
val sequence: IndexedSeq[Byte]

The nucleotide sequence.
The nucleotide sequence.

Definition Classes
PairedRead → Read
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
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( ... )

case class PairedRead[+T <: Read](read: T, isFirstInPair: Boolean, mateAlignmentProperties: Option[MateAlignmentProperties]) extends Read with Product with Serializable

Instance Constructors

new PairedRead(read: T, isFirstInPair: Boolean, mateAlignmentProperties: Option[MateAlignmentProperties])

Value Members

final def !=(arg0: AnyRef): Boolean

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: AnyRef): Boolean

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def asMappedRead: Option[MappedRead]

val baseQualities: IndexedSeq[Byte]

def clone(): AnyRef

final def eq(arg0: AnyRef): Boolean

val failedVendorQualityChecks: Boolean

def finalize(): Unit

final def getClass(): Class[_]

val isDuplicate: Boolean

val isFirstInPair: Boolean

final def isInstanceOf[T0]: Boolean

val isMapped: Boolean

val isMateMapped: Boolean

val isPaired: Boolean

val mateAlignmentProperties: Option[MateAlignmentProperties]

val name: String

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val read: T

val sampleId: SampleId

val sequence: IndexedSeq[Byte]

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

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 Read

Inherited from HasSampleId

Inherited from AnyRef

Inherited from Any

Ungrouped