class MagicBlastArgs extends cannoli.MagicBlastArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Magic-BLAST command line arguments.
Linear Supertypes
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Inherited
- MagicBlastArgs
- ParquetArgs
- CramArgs
- ADAMSaveAnyArgs
- SaveArgs
- ParquetRDDArgs
- MagicBlastArgs
- Args4jBase
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- Any
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Visibility
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Instance Constructors
- new MagicBlastArgs()
Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
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final
def
##(): Int
- Definition Classes
- AnyRef → Any
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final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
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var
addFiles: Boolean
- Definition Classes
- MagicBlastArgs
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final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
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var
asSingleFile: Boolean
- Definition Classes
- MagicBlastArgs → ADAMSaveAnyArgs
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val
blockSize: Int
- Definition Classes
- ParquetArgs → ParquetRDDArgs
- Annotations
- @Option()
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def
clone(): AnyRef
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
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val
compressionCodec: CompressionCodecName
- Definition Classes
- ParquetArgs → ParquetRDDArgs
- Annotations
- @Option()
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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
db: String
- Definition Classes
- MagicBlastArgs
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var
deferMerging: Boolean
- Definition Classes
- MagicBlastArgs → ADAMSaveAnyArgs
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val
disableDictionaryEncoding: Boolean
- Definition Classes
- ParquetArgs → ParquetRDDArgs
- Annotations
- @Option()
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var
disableFastConcat: Boolean
- Definition Classes
- MagicBlastArgs → ADAMSaveAnyArgs
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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
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var
executable: String
- Definition Classes
- MagicBlastArgs
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def
finalize(): Unit
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
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var
gapExtend: Integer
- Definition Classes
- MagicBlastArgs
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var
gapOpen: Integer
- Definition Classes
- MagicBlastArgs
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final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
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def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
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var
image: String
- Definition Classes
- MagicBlastArgs
- var inputPath: String
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
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val
logLevel: String
- Definition Classes
- ParquetArgs
- Annotations
- @Option()
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var
maxEditDistance: Integer
- Definition Classes
- MagicBlastArgs
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var
maxIntronLength: Integer
- Definition Classes
- MagicBlastArgs
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
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final
def
notify(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
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final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
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var
outputPath: String
- Definition Classes
- MagicBlastArgs → SaveArgs
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val
pageSize: Int
- Definition Classes
- ParquetArgs → ParquetRDDArgs
- Annotations
- @Option()
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var
penalty: Integer
- Definition Classes
- MagicBlastArgs
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var
percentIdentity: Double
- Definition Classes
- MagicBlastArgs
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var
score: String
- Definition Classes
- MagicBlastArgs
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var
sortFastqOutput: Boolean
- Definition Classes
- MagicBlastArgs → ADAMSaveAnyArgs
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var
stringency: String
- Definition Classes
- MagicBlastArgs
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var
sudo: Boolean
- Definition Classes
- MagicBlastArgs
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
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def
toString(): String
- Definition Classes
- AnyRef → Any
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var
transcriptome: Boolean
- Definition Classes
- MagicBlastArgs
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var
useDocker: Boolean
- Definition Classes
- MagicBlastArgs
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var
useSingularity: Boolean
- Definition Classes
- MagicBlastArgs
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final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
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final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
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final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
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var
wordSize: Integer
- Definition Classes
- MagicBlastArgs