class TransformAlignmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs with CramArgs
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Inherited
- TransformAlignmentsArgs
- CramArgs
- ParquetArgs
- ADAMSaveAnyArgs
- SaveArgs
- ParquetRDDArgs
- Args4jBase
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Instance Constructors
- new TransformAlignmentsArgs()
Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
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final
def
##(): Int
- Definition Classes
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final
def
==(arg0: Any): Boolean
- Definition Classes
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final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
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var
asSingleFile: Boolean
- Definition Classes
- TransformAlignmentsArgs → ADAMSaveAnyArgs
- var binQualityScores: String
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val
blockSize: Int
- Definition Classes
- ParquetArgs → ParquetRDDArgs
- Annotations
- @Option()
- var cache: Boolean
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def
clone(): AnyRef
- Attributes
- protected[lang]
- Definition Classes
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- Annotations
- @throws( ... ) @native() @HotSpotIntrinsicCandidate()
- var coalesce: Int
- var command: String
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val
compressionCodec: CompressionCodecName
- Definition Classes
- ParquetArgs → ParquetRDDArgs
- Annotations
- @Option()
- var concatFilename: String
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def
configureCramFormat(sc: SparkContext): Option[Unit]
Configure CRAM format.
Configure CRAM format.
- sc
Spark context to configure
- Definition Classes
- CramArgs
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val
cramReference: String
- Definition Classes
- CramArgs
- Annotations
- @Option()
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var
deferMerging: Boolean
- Definition Classes
- TransformAlignmentsArgs → ADAMSaveAnyArgs
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val
disableDictionaryEncoding: Boolean
- Definition Classes
- ParquetArgs → ParquetRDDArgs
- Annotations
- @Option()
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var
disableFastConcat: Boolean
- Definition Classes
- TransformAlignmentsArgs → ADAMSaveAnyArgs
- var disableProcessingStep: Boolean
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var
doPrintUsage: Boolean
- Definition Classes
- Args4jBase
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
- var fastqReadGroup: String
- var forceLoadBam: Boolean
- var forceLoadFastq: Boolean
- var forceLoadIFastq: Boolean
- var forceLoadParquet: Boolean
- var forceShuffle: Boolean
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final
def
getClass(): Class[_]
- Definition Classes
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- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
def
hashCode(): Int
- Definition Classes
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- Annotations
- @native() @HotSpotIntrinsicCandidate()
- var inputPath: String
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
- var knownIndelsFile: String
- var knownSnpsFile: String
- var limitProjection: Boolean
- var locallyRealign: Boolean
- var lodThreshold: Double
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val
logLevel: String
- Definition Classes
- ParquetArgs
- Annotations
- @Option()
- 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
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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final
def
notify(): Unit
- Definition Classes
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- @native() @HotSpotIntrinsicCandidate()
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final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
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var
outputPath: String
- Definition Classes
- TransformAlignmentsArgs → SaveArgs
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val
pageSize: Int
- Definition Classes
- ParquetArgs → ParquetRDDArgs
- Annotations
- @Option()
- 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
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var
sortFastqOutput: Boolean
- Definition Classes
- TransformAlignmentsArgs → ADAMSaveAnyArgs
- var storageLevel: String
- var stringency: String
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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-
def
toString(): String
- Definition Classes
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- var unclipReads: Boolean
- var useAlignedReadPredicate: Boolean
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final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
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- @throws( ... )
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final
def
wait(arg0: Long): Unit
- Definition Classes
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- @throws( ... ) @native()
-
final
def
wait(): Unit
- Definition Classes
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- Annotations
- @throws( ... )
Deprecated Value Members
-
def
finalize(): Unit
- Attributes
- protected[lang]
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- @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
- Deprecated
(Since version ) see corresponding Javadoc for more information.