Cannoli_2.12: CLI 0.12.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package cannoli
  Definition Classes
    bdgenomics
-  package cli
  Definition Classes
    cannoli
- About
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- BcftoolsCallArgs
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- BcftoolsMpileupArgs
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- BcftoolsNormArgs
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- Blastn
- BlastnArgs
- Bowtie
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- Bowtie2Args
- BowtieArgs
- BwaMem
- BwaMem2
- BwaMem2Args
- BwaMemArgs
- Cannoli
- CannoliModule
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- FreebayesArgs
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- GemArgs
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- MagicBlastArgs
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- Minimap2Args
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- SampleReadsArgs
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- SamtoolsMpileupArgs
- SingleEndBowtie2
- SingleEndBowtie2Args
- SingleEndStar
- SingleEndStarArgs
- Snap
- SnapArgs
- SnpEff
- SnpEffArgs
- Star
- StarArgs
- Vep
- VepArgs
- VtNormalize
- VtNormalizeArgs

c

org.bdgenomics.cannoli.cli

# SnpEffArgs 

###

#### class SnpEffArgs extends cannoli.SnpEffArgs with ADAMSaveAnyArgs with ParquetArgs

SnpEff command line arguments.

Linear Supertypes
ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, cannoli.SnpEffArgs, Args4jBase, AnyRef, Any
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Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. SnpEffArgs
2. ParquetArgs
3. ADAMSaveAnyArgs
4. SaveArgs
5. ParquetRDDArgs
6. SnpEffArgs
7. Args4jBase
8. AnyRef
9. Any

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Visibility

1. Public
2. All

### Instance Constructors

1.  new SnpEffArgs()

### Value Members

1.  final def !=(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
2.  final def ##(): Int
   Definition Classes
     AnyRef → Any
3.  final def ==(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
4.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
5.  var asSingleFile: Boolean
   Definition Classes
     SnpEffArgs → ADAMSaveAnyArgs
6.  val blockSize: Int
   Definition Classes
     ParquetArgs → ParquetRDDArgs
   Annotations
     @Option()
7.  def clone(): AnyRef
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native() @HotSpotIntrinsicCandidate()
8.  val compressionCodec: CompressionCodecName
   Definition Classes
     ParquetArgs → ParquetRDDArgs
   Annotations
     @Option()
9.  var database: String
   Definition Classes
     SnpEffArgs
10.  var deferMerging: Boolean
    Definition Classes
      SnpEffArgs → ADAMSaveAnyArgs
11.  val disableDictionaryEncoding: Boolean
    Definition Classes
      ParquetArgs → ParquetRDDArgs
    Annotations
      @Option()
12.  var disableFastConcat: Boolean
    Definition Classes
      SnpEffArgs → ADAMSaveAnyArgs
13.  var doPrintUsage: Boolean
    Definition Classes
      Args4jBase
14.  final def eq(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
15.  def equals(arg0: Any): Boolean
    Definition Classes
      AnyRef → Any
16.  var executable: String
    Definition Classes
      SnpEffArgs
17.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
18.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
19.  var image: String
    Definition Classes
      SnpEffArgs
20.  var inputPath: String
21.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
22.  val logLevel: String
    Definition Classes
      ParquetArgs
    Annotations
      @Option()
23.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
24.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
25.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
26.  var outputPath: String
    Definition Classes
      SnpEffArgs → SaveArgs
27.  val pageSize: Int
    Definition Classes
      ParquetArgs → ParquetRDDArgs
    Annotations
      @Option()
28.  var sortFastqOutput: Boolean
    Definition Classes
      SnpEffArgs → ADAMSaveAnyArgs
29.  var stringency: String
30.  var sudo: Boolean
    Definition Classes
      SnpEffArgs
31.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
32.  def toString(): String
    Definition Classes
      AnyRef → Any
33.  var useDocker: Boolean
    Definition Classes
      SnpEffArgs
34.  var useSingularity: Boolean
    Definition Classes
      SnpEffArgs
35.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
36.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
37.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Deprecated Value Members

1.  def finalize(): Unit
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
   Deprecated

     (Since version ) see corresponding Javadoc for more information.

### Inherited from ParquetArgs

### Inherited from ADAMSaveAnyArgs

### Inherited from SaveArgs

### Inherited from ParquetRDDArgs

### Inherited from cannoli.SnpEffArgs

### Inherited from Args4jBase

### Inherited from AnyRef

### Inherited from Any

### Ungrouped