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
final def asInstanceOf[T0]: T0

Definition Classes
Any
var bins: Int
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
var cluster: Boolean
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
def finalize(): Unit

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

Definition Classes
AnyRef → Any
def halfWindowSize: Int

Definition Classes
HalfWindowConfig
def hashCode(): Int

Definition Classes
AnyRef → Any
var includeDuplicates: Boolean

Definition Classes
ReadFilterArgs
var includeFailedQualityChecks: Boolean

Definition Classes
ReadFilterArgs
var includeSingleEnd: Boolean

Definition Classes
ReadFilterArgs
lazy val inputs: PerSample[Input]

Definition Classes
Base
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
var localOutputPath: String
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 maxReadsPerPartition: Int

Definition Classes
CappedRegionsPartitionerArgs
var minAlignmentQuality: Int

Definition Classes
ReadFilterArgs
var minReadDepth: Int
var minVAF: Int
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
var numClusters: Int
def numPartitions(sc: SparkContext): Int

Definition Classes
UniformPartitionerArgs
var onlyMappedReads: Boolean

Definition Classes
ReadFilterArgs
var output: 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
var printStats: Boolean
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 samplePercent: Int
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
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 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]

final def asInstanceOf[T0]: T0

var bins: Int

def clone(): AnyRef

var cluster: Boolean

var compressReadPartitions: Boolean

var doPrintUsage: Boolean

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

var explodeCoverage: Boolean

def finalize(): Unit

final def getClass(): Class[_]

def halfWindowSize: Int

def hashCode(): Int

var includeDuplicates: Boolean

var includeFailedQualityChecks: Boolean

var includeSingleEnd: Boolean

lazy val inputs: PerSample[Input]

final def isInstanceOf[T0]: Boolean

var localOutputPath: String

var lociFile: String

def lociFileOpt: Option[String]

var lociPartitionerName: String

def lociPartitioningPathOpt: Option[String]

var lociStr: String

def lociStrOpt: Option[String]

var maxReadsPerPartition: Int

var minAlignmentQuality: Int

var minReadDepth: Int

var minVAF: Int

final def ne(arg0: AnyRef): Boolean

var noSequenceDictionary: Boolean

final def notify(): Unit

final def notifyAll(): Unit

var numClusters: Int

def numPartitions(sc: SparkContext): Int

var onlyMappedReads: Boolean

var output: 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

var printStats: Boolean

def reference(sc: SparkContext): ReferenceBroadcast

var referenceIsPartial: Boolean

var referencePath: String

var sampleNames: Array[String]

var samplePercent: Int

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

def toString(): String

var trimRanges: Boolean

def validate(sc: SparkContext): Unit

final def wait(): Unit

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

final def wait(arg0: Long): Unit

Inherited from ReferenceArgs

Inherited from HasReference

Inherited from PartitionedRegionsArgs

Inherited from LociPartitionerArgs

Inherited from CappedRegionsPartitionerArgs

Inherited from HalfWindowConfig

Inherited from MicroRegionPartitionerArgs

Inherited from UniformPartitionerArgs

Inherited from readsets.args.Arguments

Inherited from Base

Inherited from NoSequenceDictionaryArgs

Inherited from ReadFilterArgs