GenotypesSummaryCounts

Simple counts of various properties across a set of genotypes.

Note: for counts of variants, both homozygous and heterozygous count as 1 (i.e. homozygous alternate is NOT counted as 2). This seems to be the most common convention.

genotypesCounts: Counts of genotypes: map from list of GenotypeAllele (of size ploidy) -> count
singleNucleotideVariantCounts: Map from ReferenceAndAlternate -> count where ReferenceAndAlternate is a single base variant.
multipleNucleotideVariantCount: Count of multiple nucleotide variants (e.g.: AA -> TG)
insertionCount: Count of insertions
deletionCount: Count of deletions
readCount: Sum of read depths for all genotypes with a called variant
phasedCount: Number of genotypes with phasing information

Linear Supertypes

Serializable, Serializable, Product, Equals, AnyRef, Any

Instance Constructors

new GenotypesSummaryCounts(genotypesCounts: GenotypeAlleleCounts, singleNucleotideVariantCounts: VariantCounts, multipleNucleotideVariantCount: Long, insertionCount: Long, deletionCount: Long, readCount: Option[Long], phasedCount: Long)

genotypesCounts
Counts of genotypes: map from list of GenotypeAllele (of size ploidy) -> count
singleNucleotideVariantCounts
Map from ReferenceAndAlternate -> count where ReferenceAndAlternate is a single base variant.
multipleNucleotideVariantCount
Count of multiple nucleotide variants (e.g.: AA -> TG)
insertionCount
Count of insertions
deletionCount
Count of deletions
readCount
Sum of read depths for all genotypes with a called variant
phasedCount
Number of genotypes with phasing information

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
lazy val averageReadDepthAtVariants: Option[Double]
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def combine(that: GenotypesSummaryCounts): GenotypesSummaryCounts
val deletionCount: Long

Count of deletions
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
lazy val genotypesCount: Long
val genotypesCounts: GenotypeAlleleCounts

Counts of genotypes: map from list of GenotypeAllele (of size ploidy) -> count
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
val insertionCount: Long

Count of insertions
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
val multipleNucleotideVariantCount: Long

Count of multiple nucleotide variants (e.
Count of multiple nucleotide variants (e.g.: AA -> TG)
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
lazy val noCallCount: Long
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val phasedCount: Long

Number of genotypes with phasing information
val readCount: Option[Long]

Sum of read depths for all genotypes with a called variant
lazy val singleNucleotideVariantCount: Long
val singleNucleotideVariantCounts: VariantCounts

Map from ReferenceAndAlternate -> count where ReferenceAndAlternate is a single base variant.
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
lazy val transitionCount: Long
lazy val transversionCount: Long
lazy val variantGenotypesCount: Long
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( ... )
lazy val withDefaultZeroCounts: GenotypesSummaryCounts

case class GenotypesSummaryCounts(genotypesCounts: GenotypeAlleleCounts, singleNucleotideVariantCounts: VariantCounts, multipleNucleotideVariantCount: Long, insertionCount: Long, deletionCount: Long, readCount: Option[Long], phasedCount: Long) extends Product with Serializable

Instance Constructors

new GenotypesSummaryCounts(genotypesCounts: GenotypeAlleleCounts, singleNucleotideVariantCounts: VariantCounts, multipleNucleotideVariantCount: Long, insertionCount: Long, deletionCount: Long, readCount: Option[Long], phasedCount: Long)

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

lazy val averageReadDepthAtVariants: Option[Double]

def clone(): AnyRef

def combine(that: GenotypesSummaryCounts): GenotypesSummaryCounts

val deletionCount: Long

final def eq(arg0: AnyRef): Boolean

def finalize(): Unit

lazy val genotypesCount: Long

val genotypesCounts: GenotypeAlleleCounts

final def getClass(): Class[_]

val insertionCount: Long

final def isInstanceOf[T0]: Boolean

val multipleNucleotideVariantCount: Long

final def ne(arg0: AnyRef): Boolean

lazy val noCallCount: Long

final def notify(): Unit

final def notifyAll(): Unit

val phasedCount: Long

val readCount: Option[Long]

lazy val singleNucleotideVariantCount: Long

val singleNucleotideVariantCounts: VariantCounts

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

lazy val transitionCount: Long

lazy val transversionCount: Long

lazy val variantGenotypesCount: Long

final def wait(): Unit

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

final def wait(arg0: Long): Unit

lazy val withDefaultZeroCounts: GenotypesSummaryCounts

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

Ungrouped