ADAM_2.12: CLI 1.0.1 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

o

org.bdgenomics.adam.cli

# Coverage 

###
Companion class Coverage

#### object Coverage extends BDGCommandCompanion

Coverage (accessible as the command 'coverage' through the CLI) takes two arguments, an INPUT and OUTPUT, and calculates the number of reads from INPUT at every location in the file. Optional arguments are only_negative_strands, only_positive_strands and collapse. only_negative_strands and only_positive_strands save coverage computed from only negative and positive strands, respectively. Collapse specifies whether saved coverage should merge neighboring coverage with the same counts to one record.

Linear Supertypes
BDGCommandCompanion, AnyRef, Any
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1. Coverage
2. BDGCommandCompanion
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### 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.  def apply(cmdLine: Array[String]): BDGCommand
   Definition Classes
     Coverage → BDGCommandCompanion
5.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
6.  def clone(): AnyRef
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native() @HotSpotIntrinsicCandidate()
7.  val commandDescription: String
   Definition Classes
     Coverage → BDGCommandCompanion
8.  val commandName: String
   Definition Classes
     Coverage → BDGCommandCompanion
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[_]
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      @native() @HotSpotIntrinsicCandidate()
12.  def hashCode(): Int
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      @native() @HotSpotIntrinsicCandidate()
13.  final def isInstanceOf[T0]: Boolean
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      Any
14.  def main(cmdLine: Array[String]): Unit
    Definition Classes
      BDGCommandCompanion
15.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
16.  final def notify(): Unit
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      AnyRef
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      @native() @HotSpotIntrinsicCandidate()
17.  final def notifyAll(): Unit
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      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
18.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
19.  def toString(): String
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      AnyRef → Any
20.  final def wait(arg0: Long, arg1: Int): Unit
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      @throws( ... )
21.  final def wait(arg0: Long): Unit
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      @throws( ... ) @native()
22.  final def wait(): Unit
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      @throws( ... )

### Deprecated Value Members

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

### Inherited from BDGCommandCompanion

### Inherited from AnyRef

### Inherited from Any

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