ReferenceVariant

abstract def allele: Allele

reference and sequenced bases for this variant

abstract def contigName: ContigName

Name of the reference contig

abstract def end: Locus

The end position on the genome, *exclusive*.

abstract def rsID: Option[Int]

abstract def sampleName: SampleName

abstract def start: Locus

Start position on the genome, inclusive.

abstract def toBDGGenotype: bdgenomics.formats.avro.Genotype

final def !=(arg0: AnyRef): Boolean

final def !=(arg0: Any): Boolean

final def ##(): Int

def <(that: Interval): Boolean

def <=(that: Interval): Boolean

final def ==(arg0: AnyRef): Boolean

final def ==(arg0: Any): Boolean

def >(that: Interval): Boolean

def >=(that: Interval): Boolean

final def asInstanceOf[T0]: T0

def bdgVariant: Variant

Conversion to ADAMVariant

def bdgVariantDatabase: DatabaseVariantAnnotation

def clone(): AnyRef

def compare(other: Interval): Int

Comparisons between ranges.

def compareTo(that: Interval): Int

def contains(locus: Locus): Boolean

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

def iterator(): Iterator[Long]

Iterate through elements in the range.

def length: NumLoci

Number of elements in the range.

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def overlaps(other: ReferenceRegion): Boolean

Does the region overlap another reference region

def overlapsLocus(locus: Locus, halfWindowSize: Int = 0): Boolean

Does the region overlap the given locus, with halfWindowSize padding?

def regionStr: String

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