TransformAlignmentsArgs

Instance Constructors

new TransformAlignmentsArgs()

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

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

Definition Classes
AnyRef → Any
final def asInstanceOf[T0]: T0

Definition Classes
Any
var asSingleFile: Boolean

Definition Classes
TransformAlignmentsArgs → ADAMSaveAnyArgs
var binQualityScores: String
var blockSize: Int

Definition Classes
ParquetArgs → ParquetRDDArgs
var cache: Boolean
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
var coalesce: Int
var command: String
var compressionCodec: CompressionCodecName

Definition Classes
ParquetArgs → ParquetRDDArgs
var concatFilename: String
var deferMerging: Boolean

Definition Classes
TransformAlignmentsArgs → ADAMSaveAnyArgs
var disableDictionaryEncoding: Boolean

Definition Classes
ParquetArgs → ParquetRDDArgs
var disableFastConcat: Boolean

Definition Classes
TransformAlignmentsArgs → ADAMSaveAnyArgs
var disableProcessingStep: Boolean
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 fastqReadGroup: String
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
var forceLoadBam: Boolean
var forceLoadFastq: Boolean
var forceLoadIFastq: Boolean
var forceLoadParquet: Boolean
var forceShuffle: Boolean
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def hashCode(): Int

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

Definition Classes
Any
var knownIndelsFile: String
var knownSnpsFile: String
var limitProjection: Boolean
var locallyRealign: Boolean
var lodThreshold: Double
var logLevel: String

Definition Classes
ParquetArgs
var markDuplicates: Boolean
var maxConsensusNumber: Int
var maxIndelSize: Int
var maxReadLength: Int
var maxReadsPerTarget: Int
var maxTargetSize: Int
var mdTagsFragmentSize: Long
var mdTagsOverwrite: Boolean
var mdTagsReferenceFile: String
var minAcceptableQuality: Int
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
var outputPath: String

Definition Classes
TransformAlignmentsArgs → SaveArgs
var pageSize: Int

Definition Classes
ParquetArgs → ParquetRDDArgs
var pairedFastqFile: String
var partitionByStartPos: Boolean
var partitionedBinSize: Int
var recalibrateBaseQualities: Boolean
var reference: String
var regionPredicate: String
var repartition: Int
var samplingFraction: Double
var samplingSeed: Long
var sortByReadName: Boolean
var sortByReferencePosition: Boolean
var sortByReferencePositionAndIndex: Boolean
var sortFastqOutput: Boolean

Definition Classes
TransformAlignmentsArgs → ADAMSaveAnyArgs
var storageLevel: String
var stringency: String
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Definition Classes
AnyRef → Any
var unclipReads: Boolean
var useAlignedReadPredicate: Boolean
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( ... )

Related Doc: package cli

class TransformAlignmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

Instance Constructors

new TransformAlignmentsArgs()

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

var asSingleFile: Boolean

var binQualityScores: String

var blockSize: Int

var cache: Boolean

def clone(): AnyRef

var coalesce: Int

var command: String

var compressionCodec: CompressionCodecName

var concatFilename: String

var deferMerging: Boolean

var disableDictionaryEncoding: Boolean

var disableFastConcat: Boolean

var disableProcessingStep: Boolean

var doPrintUsage: Boolean

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

var fastqReadGroup: String

def finalize(): Unit

var forceLoadBam: Boolean

var forceLoadFastq: Boolean

var forceLoadIFastq: Boolean

var forceLoadParquet: Boolean

var forceShuffle: Boolean

final def getClass(): Class[_]

def hashCode(): Int

var inputPath: String

final def isInstanceOf[T0]: Boolean

var knownIndelsFile: String

var knownSnpsFile: String

var limitProjection: Boolean

var locallyRealign: Boolean

var lodThreshold: Double

var logLevel: String

var markDuplicates: Boolean

var maxConsensusNumber: Int

var maxIndelSize: Int

var maxReadLength: Int

var maxReadsPerTarget: Int

var maxTargetSize: Int

var mdTagsFragmentSize: Long

var mdTagsOverwrite: Boolean

var mdTagsReferenceFile: String

var minAcceptableQuality: Int

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

var outputPath: String

var pageSize: Int

var pairedFastqFile: String

var partitionByStartPos: Boolean

var partitionedBinSize: Int

var recalibrateBaseQualities: Boolean

var reference: String

var regionPredicate: String

var repartition: Int

var samplingFraction: Double

var samplingSeed: Long

var sortByReadName: Boolean

var sortByReferencePosition: Boolean

var sortByReferencePositionAndIndex: Boolean

var sortFastqOutput: Boolean

var storageLevel: String

var stringency: String

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

def toString(): String

var unclipReads: Boolean

var useAlignedReadPredicate: Boolean

final def wait(): Unit

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

final def wait(arg0: Long): Unit