ReferenceGenome

abstract def getContig(contigName: String): ContigSequence

Retrieve a full contig/chromosome sequence

abstract def getReferenceBase(contigName: String, locus: Int): Byte

Retrieve a reference base on a given contig at a given locus

abstract def getReferenceSequence(contigName: String, startLocus: Int, endLocus: Int): Array[Byte]

Get the reference base at the given reference location

abstract val source: Option[String]

Path where this reference was loaded from, or other description of its provenance (optional).

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 buildMdTag(readSequence: String, referenceContig: String, referenceStart: Int, cigar: Cigar): String

Build a new MDTag from the reference and read sequence

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