ADAM_2.12: CLI 1.0 API < Back
 

# 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

# Coverage 

###
Companion object Coverage

#### class Coverage extends BDGSparkCommand[CoverageArgs]

Linear Supertypes
BDGSparkCommand[CoverageArgs], Logging, BDGCommand, Runnable, AnyRef, Any
 
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. Coverage
2. BDGSparkCommand
3. Logging
4. BDGCommand
5. Runnable
6. AnyRef
7. Any

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Visibility

1. Public
2. All

### Instance Constructors

1.  new Coverage(args: CoverageArgs)

### 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.  val args: CoverageArgs
   Attributes
     protected
   Definition Classes
     Coverage → BDGSparkCommand
5.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
6.  def clone(): AnyRef
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native()
7.  val companion: BDGCommandCompanion
   Definition Classes
     Coverage → BDGCommand
8.  def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
   Attributes
     protected
   Definition Classes
     Logging
9.  def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
   Attributes
     protected
   Definition Classes
     Logging
10.  def debug(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
11.  final def eq(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
12.  def equals(arg0: Any): Boolean
    Definition Classes
      AnyRef → Any
13.  def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
14.  def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
15.  def error(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
16.  def finalize(): Unit
    Attributes
      protected[lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )
17.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
18.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
19.  def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
20.  def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
21.  def info(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
22.  def isDebugEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
23.  def isErrorEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
24.  def isInfoEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
25.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
26.  def isTraceEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
27.  def isWarnEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
28.  def logger: Logger
    Attributes
      protected
    Definition Classes
      Logging
29.  def loggerName: String
    Attributes
      protected
    Definition Classes
      Logging
30.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
31.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
32.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
33.  def run(sc: SparkContext): Unit
    Definition Classes
      Coverage → BDGSparkCommand
34.  def run(): Unit
    Definition Classes
      BDGSparkCommand → Runnable
35.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
36.  def toString(): String
    Definition Classes
      AnyRef → Any
37.  def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
38.  def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
39.  def trace(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
40.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
41.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
42.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
43.  def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
44.  def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
45.  def warn(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging

### Inherited from BDGSparkCommand[CoverageArgs]

### Inherited from Logging

### Inherited from BDGCommand

### Inherited from Runnable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped