CalledAllele

Instance Constructors

new CalledAllele(sampleName: SampleName, contigName: ContigName, start: Locus, allele: Allele, evidence: AlleleEvidence, rsID: Option[Int] = scala.None, length: NumLoci = 1)

sampleName
sample the variant was called on
contigName
chromosome or genome contig of the variant
start
start position of the variant (0-based)
allele
allele (ref + seq bases) for this variant
evidence
supporting statistics for the variant
length
length of the variant

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
def <(that: Interval): Boolean

Definition Classes
Ordered
def <=(that: Interval): Boolean

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

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

Definition Classes
Any
def >(that: Interval): Boolean

Definition Classes
Ordered
def >=(that: Interval): Boolean

Definition Classes
Ordered
val allele: Allele

allele (ref + seq bases) for this variant
allele (ref + seq bases) for this variant

Definition Classes
CalledAllele → ReferenceVariant
final def asInstanceOf[T0]: T0

Definition Classes
Any
def bdgVariant: Variant

Conversion to ADAMVariant
Conversion to ADAMVariant

Definition Classes
ReferenceVariant
def bdgVariantDatabase: DatabaseVariantAnnotation

Definition Classes
ReferenceVariant
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def compare(other: Interval): Int

Comparisons between ranges.
Comparisons between ranges. Order is DESCENDING (i.e. reversed) from by start.

Definition Classes
Interval → Ordered
def compareTo(that: Interval): Int

Definition Classes
Ordered → Comparable
def contains(locus: Locus): Boolean

Definition Classes
Interval
val contigName: ContigName

chromosome or genome contig of the variant
chromosome or genome contig of the variant

Definition Classes
CalledAllele → ReferenceRegion → HasContig
val end: Locus

The end position on the genome, *exclusive*.
The end position on the genome, *exclusive*. Must be non-negative.

Definition Classes
CalledAllele → Interval
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
val evidence: AlleleEvidence

supporting statistics for the variant
def finalize(): Unit

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

Definition Classes
AnyRef → Any
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def iterator(): Iterator[Long]

Iterate through elements in the range.
Iterate through elements in the range.

Definition Classes
Interval
val length: NumLoci

length of the variant
length of the variant

Definition Classes
CalledAllele → Interval
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
def overlaps(other: ReferenceRegion): Boolean

Does the region overlap another reference region
Does the region overlap another reference region
other
another region on the genome
returns
True if the the regions overlap

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

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

Definition Classes
ReferenceRegion
def regionStr: String

Definition Classes
ReferenceRegion
val rsID: Option[Int]

Definition Classes
CalledAllele → ReferenceVariant
val sampleName: SampleName

sample the variant was called on
sample the variant was called on

Definition Classes
CalledAllele → ReferenceVariant
val start: Locus

start position of the variant (0-based)
start position of the variant (0-based)

Definition Classes
CalledAllele → Interval
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toBDGGenotype: bdgenomics.formats.avro.Genotype

Definition Classes
CalledAllele → ReferenceVariant
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 CalledAllele(sampleName: SampleName, contigName: ContigName, start: Locus, allele: Allele, evidence: AlleleEvidence, rsID: Option[Int] = scala.None, length: NumLoci = 1) extends ReferenceVariant with Product with Serializable

Instance Constructors

new CalledAllele(sampleName: SampleName, contigName: ContigName, start: Locus, allele: Allele, evidence: AlleleEvidence, rsID: Option[Int] = scala.None, length: NumLoci = 1)

Value Members

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

val allele: Allele

final def asInstanceOf[T0]: T0

def bdgVariant: Variant

def bdgVariantDatabase: DatabaseVariantAnnotation

def clone(): AnyRef

def compare(other: Interval): Int

def compareTo(that: Interval): Int

def contains(locus: Locus): Boolean

val contigName: ContigName

val end: Locus

final def eq(arg0: AnyRef): Boolean

val evidence: AlleleEvidence

def finalize(): Unit

final def getClass(): Class[_]

final def isInstanceOf[T0]: Boolean

def iterator(): Iterator[Long]

val length: NumLoci

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def overlaps(other: ReferenceRegion): Boolean

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

def regionStr: String

val rsID: Option[Int]

val sampleName: SampleName

val start: Locus

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

def toBDGGenotype: bdgenomics.formats.avro.Genotype

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 ReferenceVariant

Inherited from ReferenceRegion

Inherited from Interval

Inherited from Ordered[Interval]

Inherited from Comparable[Interval]

Inherited from HasContig

Inherited from AnyRef

Inherited from Any

Ungrouped