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 blockSize: Int

Definition Classes
ParquetArgs → ParquetRDDArgs
def clone(): AnyRef

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

Definition Classes
PartitionedRegionsArgs
var compressionCodec: CompressionCodecName

Definition Classes
ParquetArgs → ParquetRDDArgs
var dbSnpVcf: String
var debugGenotypeFilters: Boolean

Definition Classes
SomaticGenotypeFilterArguments
var disableDictionaryEncoding: Boolean

Definition Classes
ParquetArgs → ParquetRDDArgs
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 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 logLevel: String

Definition Classes
ParquetArgs
var maxGenotypes: Int

Definition Classes
GenotypeOutputArgs
var maxReadsPerPartition: Int

Definition Classes
CappedRegionsPartitionerArgs
var maxTumorReadDepth: Int

Definition Classes
SomaticGenotypeFilterArguments
var maximumMedianMismatches: Int

Definition Classes
SomaticGenotypeFilterArguments
var minAlignmentQuality: Int

Definition Classes
ReadFilterArgs
var minAverageBaseQuality: Int

Definition Classes
SomaticGenotypeFilterArguments
var minAverageMappingQuality: Int

Definition Classes
SomaticGenotypeFilterArguments
var minLOD: Int

Definition Classes
SomaticGenotypeFilterArguments
var minLikelihood: Int

Definition Classes
SomaticGenotypeFilterArguments
var minNormalReadDepth: Int

Definition Classes
SomaticGenotypeFilterArguments
var minTumorAlternateReadDepth: Int

Definition Classes
SomaticGenotypeFilterArguments
var minTumorReadDepth: Int

Definition Classes
SomaticGenotypeFilterArguments
var minVAF: Int

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

Definition Classes
AnyRef
var noSequenceDictionary: Boolean

Definition Classes
NoSequenceDictionaryArgs
var normalReads: String

Definition Classes
TumorNormalReadsArgs
val normalSampleName: String

Definition Classes
TumorNormalReadsArgs
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

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

Definition Classes
UniformPartitionerArgs
var oddsThreshold: Int
var onlyMappedReads: Boolean

Definition Classes
ReadFilterArgs
var outChunks: Int

Definition Classes
GenotypeOutputArgs
lazy val outputPathStr: String

Definition Classes
GenotypeOutputArgs
var pageSize: Int

Definition Classes
ParquetArgs → ParquetRDDArgs
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
def paths: Array[String]

Definition Classes
TumorNormalReadsArgs → 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
def sampleNames: Array[String]

Definition Classes
TumorNormalReadsArgs → Base
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Definition Classes
AnyRef → Any
var trimRanges: Boolean

Definition Classes
CappedRegionsPartitionerArgs
var tumorReads: String

Definition Classes
TumorNormalReadsArgs
val tumorSampleName: String

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

Perform validation of command line arguments at startup.
Perform validation of command line arguments at startup. This allows some late failures (e.g. output file already exists) to be surfaced more quickly.

Definition Classes
GenotypeOutputArgs
var variantOutput: String

Definition Classes
GenotypeOutputArgs
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( ... )
def writeVariants(genotypes: GenotypeRDD): Unit

Write out an RDD of Genotype instances to a file.
Write out an RDD of Genotype instances to a file.
genotypes
ADAM genotypes (i.e. the variants)

Definition Classes
GenotypeOutputArgs

class Arguments extends Args4jBase with Args with TumorNormalReadsArgs with PartitionedRegionsArgs with SomaticGenotypeFilterArguments with GenotypeOutputArgs 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 blockSize: Int

def clone(): AnyRef

var compressReadPartitions: Boolean

var compressionCodec: CompressionCodecName

var dbSnpVcf: String

var debugGenotypeFilters: Boolean

var disableDictionaryEncoding: 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 lociFile: String

def lociFileOpt: Option[String]

var lociPartitionerName: String

def lociPartitioningPathOpt: Option[String]

var lociStr: String

def lociStrOpt: Option[String]

var logLevel: String

var maxGenotypes: Int

var maxReadsPerPartition: Int

var maxTumorReadDepth: Int

var maximumMedianMismatches: Int

var minAlignmentQuality: Int

var minAverageBaseQuality: Int

var minAverageMappingQuality: Int

var minLOD: Int

var minLikelihood: Int

var minNormalReadDepth: Int

var minTumorAlternateReadDepth: Int

var minTumorReadDepth: Int

var minVAF: Int

final def ne(arg0: AnyRef): Boolean

var noSequenceDictionary: Boolean

var normalReads: String

val normalSampleName: String

final def notify(): Unit

final def notifyAll(): Unit

def numPartitions(sc: SparkContext): Int

var oddsThreshold: Int

var onlyMappedReads: Boolean

var outChunks: Int

lazy val outputPathStr: String

var pageSize: Int

var parallelism: NumPartitions

def parseFilters(hadoopConfiguration: Configuration): InputFilters

def partitionedReadsPathOpt: Option[String]

var partitioningAccuracy: NumMicroPartitions

def paths: Array[String]

var printMetrics: Boolean

var printPartitioningStats: Boolean

def reference(sc: SparkContext): ReferenceBroadcast

var referenceIsPartial: Boolean

var referencePath: String

def sampleNames: Array[String]

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

def toString(): String

var trimRanges: Boolean

var tumorReads: String

val tumorSampleName: String