ADAM_2.12: CLI 0.36.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package cli
  Definition Classes
    adam
- ADAM2Fastq
- ADAM2FastqArgs
- ADAMMain
- ADAMModule
- About
- CommandGroup
- CountReadKmers
- CountReadKmersArgs
- CountSliceKmers
- CountSliceKmersArgs
- Coverage
- CoverageArgs
- FlagStat
- FlagStatArgs
- MergeShards
- MergeShardsArgs
- PrintADAM
- PrintADAMArgs
- TransformAlignments
- TransformAlignmentsArgs
- TransformFeatures
- TransformFeaturesArgs
- TransformFragments
- TransformFragmentsArgs
- TransformGenotypes
- TransformGenotypesArgs
- TransformSequences
- TransformSequencesArgs
- TransformSlices
- TransformSlicesArgs
- TransformVariants
- TransformVariantsArgs
- View
- ViewArgs

c

org.bdgenomics.adam.cli

# FlagStatArgs 

###

#### class FlagStatArgs extends Args4jBase with CramArgs

Linear Supertypes
CramArgs, Args4jBase, AnyRef, Any
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Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. FlagStatArgs
2. CramArgs
3. Args4jBase
4. AnyRef
5. Any

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Visibility

1. Public
2. All

### Instance Constructors

1.  new FlagStatArgs()

### 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.  def clone(): AnyRef
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native() @HotSpotIntrinsicCandidate()
6.  def configureCramFormat(sc: SparkContext): Option[Unit]

   Configure CRAM format.

   Configure CRAM format.

   sc

     Spark context to configure

   Definition Classes
     CramArgs
7.  val cramReference: String
   Definition Classes
     CramArgs
   Annotations
     @Option()
8.  var doPrintUsage: Boolean
   Definition Classes
     Args4jBase
9.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
10.  def equals(arg0: Any): Boolean
    Definition Classes
      AnyRef → Any
11.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
12.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
13.  var inputPath: String
14.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
15.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
16.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
17.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
18.  var outputPath: String
19.  var stringency: String
20.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
21.  def toString(): String
    Definition Classes
      AnyRef → Any
22.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
23.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
24.  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 CramArgs

### Inherited from Args4jBase

### Inherited from AnyRef

### Inherited from Any

### Ungrouped