Arguments

Instance Constructors

new Arguments()

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
var _lociPartitioningPathOpt: Option[String]

Attributes
protected
Definition Classes
LociPartitionerArgs
var analytes: Array[String]

Definition Classes
Arguments
var anyAlleleMinSupportingPercent: Double

Definition Classes
CommandlineArguments
var anyAlleleMinSupportingReads: Int

Definition Classes
CommandlineArguments
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
var compressReadPartitions: Boolean

Definition Classes
PartitionedRegionsArgs
var doPrintUsage: Boolean

Definition Classes
Args4jBase
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def equals(arg0: Any): Boolean

Definition Classes
AnyRef → Any
var explodeCoverage: Boolean

Definition Classes
CappedRegionsPartitionerArgs
var filterSomaticNormalDepth: Int

Definition Classes
CommandlineArguments
var filterSomaticNormalNonreferencePercent: Double

Definition Classes
CommandlineArguments
var filterStrandBiasPhred: Double

Definition Classes
CommandlineArguments
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
var forceCallLociFile: String

Attributes
protected
Definition Classes
ForceCallLociArgs
def forceCallLociFileOpt: Option[String]

Definition Classes
ForceCallLociArgs
var forceCallLociStr: String

Attributes
protected
Definition Classes
ForceCallLociArgs
def forceCallLociStrOpt: Option[String]

Definition Classes
ForceCallLociArgs
var germlineNegativeLog10HeterozygousPrior: Double

Definition Classes
CommandlineArguments
var germlineNegativeLog10HomozygousAlternatePrior: Double

Definition Classes
CommandlineArguments
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def halfWindowSize: Int

Definition Classes
HalfWindowConfig
def hashCode(): Int

Definition Classes
AnyRef → Any
var headerMetadata: Array[String]
var includeDuplicates: Boolean

Definition Classes
ReadFilterArgs
var includeFailedQualityChecks: Boolean

Definition Classes
ReadFilterArgs
var includeFiltered: Boolean
var includeSingleEnd: Boolean

Definition Classes
ReadFilterArgs
lazy val inputs: PerSample[Input]

Definition Classes
Base
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
var lociFile: String

Attributes
protected
Definition Classes
CallLociArgs
def lociFileOpt: Option[String]

Definition Classes
CallLociArgs
var lociPartitionerName: String

Attributes
protected
Definition Classes
LociPartitionerArgs
def lociPartitioningPathOpt: Option[String]

Simple getter interface here supports overriding behavior here to support different resolution logic, cf.
Simple getter interface here supports overriding behavior here to support different resolution logic, cf. PartitionedRegionsArgs.

Definition Classes
PartitionedRegionsArgs → LociPartitionerArgs
var lociStr: String

Attributes
protected
Definition Classes
CallLociArgs
def lociStrOpt: Option[String]

Definition Classes
CallLociArgs
var maxAllelesPerSite: Int

Definition Classes
CommandlineArguments
var maxCallsPerSite: Int

Definition Classes
CommandlineArguments
var maxReadsPerPartition: Int

Definition Classes
CappedRegionsPartitionerArgs
var minAlignmentQuality: Int

Definition Classes
ReadFilterArgs
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
var noSequenceDictionary: Boolean

Definition Classes
NoSequenceDictionaryArgs
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
def numPartitions(sc: SparkContext): Int

Definition Classes
UniformPartitionerArgs
var onlyMappedReads: Boolean

Definition Classes
ReadFilterArgs
var onlySomatic: Boolean
var out: String
var outDir: String
var parallelism: NumPartitions

Attributes
protected
Definition Classes
UniformPartitionerArgs
def parseFilters(hadoopConfiguration: Configuration): InputFilters

Definition Classes
ReadFilterArgs
def partitionedReadsPathOpt: Option[String]

Definition Classes
PartitionedRegionsArgs
var partitioningAccuracy: NumMicroPartitions

Long >= 1.
Long >= 1. Number of micro-partitions generated for each of the numPartitions Spark partitions that will be computed. Higher values of this will result in a more exact but more expensive computation. In the extreme, setting this to greater than the number of loci (per partition) will result in an exact calculation.

Definition Classes
MicroRegionPartitionerArgs
var paths: Array[String]

Definition Classes
Arguments → Base
var printMetrics: Boolean

Definition Classes
Args4jBase
var printPartitioningStats: Boolean

Definition Classes
LociPartitionerArgs
def reference(sc: SparkContext): ReferenceBroadcast

Definition Classes
HasReference
var referenceIsPartial: Boolean

Definition Classes
ReferenceArgs → HasReference
var referencePath: String

Definition Classes
ReferenceArgs → HasReference
var sampleNames: Array[String]

Definition Classes
Arguments → Base
var somaticGenotypePolicy: String

Definition Classes
CommandlineArguments
var somaticMaxGermlineErrorRatePercent: Double

Definition Classes
CommandlineArguments
var somaticNegativeLog10VariantPrior: Double

Definition Classes
CommandlineArguments
var somaticNegativeLog10VariantPriorRna: Double

Definition Classes
CommandlineArguments
var somaticNegativeLog10VariantPriorWithRnaEvidence: Double

Definition Classes
CommandlineArguments
var somaticVafFloor: Double

Definition Classes
CommandlineArguments
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
var tissueTypes: Array[String]

Definition Classes
Arguments
def toString(): String

Definition Classes
AnyRef → Any
var trimRanges: Boolean

Definition Classes
CappedRegionsPartitionerArgs
def validate(sc: SparkContext): Unit

Definition Classes
Args
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( ... )

class Arguments extends Args4jBase with Args with readsets.args.Arguments with PartitionedRegionsArgs with CommandlineArguments with jointcaller.InputCollection.Arguments with ForceCallLociArgs with ReferenceArgs

Instance Constructors

new Arguments()

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

var _lociPartitioningPathOpt: Option[String]

var analytes: Array[String]

var anyAlleleMinSupportingPercent: Double

var anyAlleleMinSupportingReads: Int

final def asInstanceOf[T0]: T0

def clone(): AnyRef

var compressReadPartitions: Boolean

var doPrintUsage: Boolean

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

var explodeCoverage: Boolean

var filterSomaticNormalDepth: Int

var filterSomaticNormalNonreferencePercent: Double

var filterStrandBiasPhred: Double

def finalize(): Unit

var forceCallLociFile: String

def forceCallLociFileOpt: Option[String]

var forceCallLociStr: String

def forceCallLociStrOpt: Option[String]

var germlineNegativeLog10HeterozygousPrior: Double

var germlineNegativeLog10HomozygousAlternatePrior: Double

final def getClass(): Class[_]

def halfWindowSize: Int

def hashCode(): Int

var headerMetadata: Array[String]

var includeDuplicates: Boolean

var includeFailedQualityChecks: Boolean

var includeFiltered: Boolean

var includeSingleEnd: Boolean

lazy val inputs: PerSample[Input]

final def isInstanceOf[T0]: Boolean

var lociFile: String

def lociFileOpt: Option[String]

var lociPartitionerName: String

def lociPartitioningPathOpt: Option[String]

var lociStr: String

def lociStrOpt: Option[String]

var maxAllelesPerSite: Int

var maxCallsPerSite: Int

var maxReadsPerPartition: Int

var minAlignmentQuality: Int

final def ne(arg0: AnyRef): Boolean

var noSequenceDictionary: Boolean

final def notify(): Unit

final def notifyAll(): Unit

def numPartitions(sc: SparkContext): Int

var onlyMappedReads: Boolean

var onlySomatic: Boolean

var out: String

var outDir: String

var parallelism: NumPartitions

def parseFilters(hadoopConfiguration: Configuration): InputFilters

def partitionedReadsPathOpt: Option[String]

var partitioningAccuracy: NumMicroPartitions

var paths: Array[String]

var printMetrics: Boolean

var printPartitioningStats: Boolean

def reference(sc: SparkContext): ReferenceBroadcast

var referenceIsPartial: Boolean

var referencePath: String

var sampleNames: Array[String]

var somaticGenotypePolicy: String

var somaticMaxGermlineErrorRatePercent: Double

var somaticNegativeLog10VariantPrior: Double

var somaticNegativeLog10VariantPriorRna: Double

var somaticNegativeLog10VariantPriorWithRnaEvidence: Double

var somaticVafFloor: Double

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

var tissueTypes: Array[String]

def toString(): String