class LongMinimap2Args extends cannoli.Minimap2Args with ADAMSaveAnyArgs with ParquetArgs
Long read Minimap2 command line arguments.
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Inherited
- LongMinimap2Args
- ParquetArgs
- ADAMSaveAnyArgs
- SaveArgs
- ParquetRDDArgs
- Minimap2Args
- ReadGroupArgs
- Args4jBase
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Instance Constructors
- new LongMinimap2Args()
Value Members
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
- Definition Classes
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final
def
==(arg0: Any): Boolean
- Definition Classes
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var
addFiles: Boolean
- Definition Classes
- Minimap2Args
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final
def
asInstanceOf[T0]: T0
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var
asSingleFile: Boolean
- Definition Classes
- LongMinimap2Args → ADAMSaveAnyArgs
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val
blockSize: Int
- Definition Classes
- ParquetArgs → ParquetRDDArgs
- Annotations
- @Option()
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def
clone(): AnyRef
- Attributes
- protected[lang]
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- @throws( ... ) @native()
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val
compressionCodec: CompressionCodecName
- Definition Classes
- ParquetArgs → ParquetRDDArgs
- Annotations
- @Option()
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def
createReadGroup(): ReadGroup
- Definition Classes
- ReadGroupArgs
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var
deferMerging: Boolean
- Definition Classes
- LongMinimap2Args → ADAMSaveAnyArgs
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val
disableDictionaryEncoding: Boolean
- Definition Classes
- ParquetArgs → ParquetRDDArgs
- Annotations
- @Option()
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var
disableFastConcat: Boolean
- Definition Classes
- LongMinimap2Args → ADAMSaveAnyArgs
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var
doPrintUsage: Boolean
- Definition Classes
- Args4jBase
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
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def
equals(arg0: Any): Boolean
- Definition Classes
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var
executable: String
- Definition Classes
- Minimap2Args
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def
finalize(): Unit
- Attributes
- protected[lang]
- Definition Classes
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- Annotations
- @throws( classOf[java.lang.Throwable] )
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var
flowOrder: String
- Definition Classes
- ReadGroupArgs
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final
def
getClass(): Class[_]
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- Annotations
- @native()
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def
hashCode(): Int
- Definition Classes
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- Annotations
- @native()
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var
image: String
- Definition Classes
- Minimap2Args
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var
indexPath: String
- Definition Classes
- Minimap2Args
- var inputPath: String
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
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var
keySequence: String
- Definition Classes
- ReadGroupArgs
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var
library: String
- Definition Classes
- ReadGroupArgs
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val
logLevel: String
- Definition Classes
- ParquetArgs
- Annotations
- @Option()
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var
minimap2Args: String
- Definition Classes
- Minimap2Args
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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- @native()
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final
def
notifyAll(): Unit
- Definition Classes
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- @native()
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var
outputPath: String
- Definition Classes
- LongMinimap2Args → SaveArgs
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val
pageSize: Int
- Definition Classes
- ParquetArgs → ParquetRDDArgs
- Annotations
- @Option()
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var
platform: String
- Definition Classes
- ReadGroupArgs
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var
platformModel: String
- Definition Classes
- ReadGroupArgs
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var
platformUnit: String
- Definition Classes
- ReadGroupArgs
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var
predictedMedianInsertSize: Integer
- Definition Classes
- ReadGroupArgs
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var
preset: String
- Definition Classes
- Minimap2Args
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var
readGroup: ReadGroup
- Definition Classes
- ReadGroupArgs
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var
readGroupId: String
- Definition Classes
- ReadGroupArgs
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var
runDate: Long
- Definition Classes
- ReadGroupArgs
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var
sampleId: String
- Definition Classes
- ReadGroupArgs
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var
seed: Integer
- Definition Classes
- Minimap2Args
- var sequenceDictionary: String
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var
sequencingCenter: String
- Definition Classes
- ReadGroupArgs
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var
sortFastqOutput: Boolean
- Definition Classes
- LongMinimap2Args → ADAMSaveAnyArgs
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var
sudo: Boolean
- Definition Classes
- Minimap2Args
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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
useDocker: Boolean
- Definition Classes
- Minimap2Args
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var
useSingularity: Boolean
- Definition Classes
- Minimap2Args
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final
def
wait(): Unit
- Definition Classes
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- @throws( ... )
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final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
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- Annotations
- @throws( ... )
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final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()