Read

abstract def asMappedRead: Option[MappedRead]

abstract def baseQualities: IndexedSeq[Byte]

The base qualities, phred scaled.

abstract def failedVendorQualityChecks: Boolean

Whether the read failed predefined vendor checks for quality

abstract def isDuplicate: Boolean

Is this read a duplicate of another?

abstract def isMapped: Boolean

Is this read mapped?

abstract def isPaired: Boolean

Whether read is from a paired-end library

abstract def name: String

abstract def sampleId: SampleId

abstract def sequence: IndexedSeq[Byte]

The nucleotide sequence.

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 clone(): AnyRef

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

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

def toString(): String

final def wait(): Unit

final def wait(arg0: Long, arg1: Int): Unit

final def wait(arg0: Long): Unit