ADAM_2.12: APIs for Java, Python 0.37.0 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 api
  Definition Classes
    adam
-  package java
  Definition Classes
    api
- AlignmentsToAlignmentsConverter
- AlignmentsToCoverageConverter
- AlignmentsToCoverageDatasetConverter
- AlignmentsToFeaturesConverter
- AlignmentsToFeaturesDatasetConverter
- AlignmentsToFragmentsConverter
- AlignmentsToFragmentsDatasetConverter
- AlignmentsToGenotypesConverter
- AlignmentsToGenotypesDatasetConverter
- AlignmentsToReadsConverter
- AlignmentsToReadsDatasetConverter
- AlignmentsToSequencesConverter
- AlignmentsToSequencesDatasetConverter
- AlignmentsToSlicesConverter
- AlignmentsToSlicesDatasetConverter
- AlignmentsToVariantContextConverter
- AlignmentsToVariantsConverter
- AlignmentsToVariantsDatasetConverter
- CoverageToAlignmentsConverter
- CoverageToAlignmentsDatasetConverter
- CoverageToCoverageConverter
- CoverageToFeaturesConverter
- CoverageToFeaturesDatasetConverter
- CoverageToFragmentsConverter
- CoverageToFragmentsDatasetConverter
- CoverageToGenotypesConverter
- CoverageToGenotypesDatasetConverter
- CoverageToReadsConverter
- CoverageToReadsDatasetConverter
- CoverageToSequencesConverter
- CoverageToSequencesDatasetConverter
- CoverageToSlicesConverter
- CoverageToSlicesDatasetConverter
- CoverageToVariantContextConverter
- CoverageToVariantsConverter
- CoverageToVariantsDatasetConverter
- FeaturesToAlignmentsConverter
- FeaturesToAlignmentsDatasetConverter
- FeaturesToCoverageConverter
- FeaturesToCoverageDatasetConverter
- FeaturesToFeatureConverter
- FeaturesToFragmentsConverter
- FeaturesToFragmentsDatasetConverter
- FeaturesToGenotypesConverter
- FeaturesToGenotypesDatasetConverter
- FeaturesToReadsConverter
- FeaturesToReadsDatasetConverter
- FeaturesToSequencesConverter
- FeaturesToSequencesDatasetConverter
- FeaturesToSlicesConverter
- FeaturesToSlicesDatasetConverter
- FeaturesToVariantContextConverter
- FeaturesToVariantsConverter
- FeaturesToVariantsDatasetConverter
- FragmentsToAlignmentsConverter
- FragmentsToAlignmentsDatasetConverter
- FragmentsToCoverageConverter
- FragmentsToCoverageDatasetConverter
- FragmentsToFeaturesConverter
- FragmentsToFeaturesDatasetConverter
- FragmentsToFragmentsConverter
- FragmentsToGenotypesConverter
- FragmentsToGenotypesDatasetConverter
- FragmentsToReadsConverter
- FragmentsToReadsDatasetConverter
- FragmentsToSequencesConverter
- FragmentsToSequencesDatasetConverter
- FragmentsToSlicesConverter
- FragmentsToSlicesDatasetConverter
- FragmentsToVariantContextConverter
- FragmentsToVariantsConverter
- FragmentsToVariantsDatasetConverter
- GenotypesToAlignmentsConverter
- GenotypesToAlignmentsDatasetConverter
- GenotypesToCoverageConverter
- GenotypesToCoverageDatasetConverter
- GenotypesToFeaturesConverter
- GenotypesToFeaturesDatasetConverter
- GenotypesToFragmentsConverter
- GenotypesToFragmentsDatasetConverter
- GenotypesToGenotypesConverter
- GenotypesToReadsConverter
- GenotypesToReadsDatasetConverter
- GenotypesToSequencesConverter
- GenotypesToSequencesDatasetConverter
- GenotypesToSlicesConverter
- GenotypesToSlicesDatasetConverter
- GenotypesToVariantContextConverter
- GenotypesToVariantsConverter
- GenotypesToVariantsDatasetConverter
- JavaADAMContext
- ReadsToAlignmentsConverter
- ReadsToAlignmentsDatasetConverter
- ReadsToCoverageConverter
- ReadsToCoverageDatasetConverter
- ReadsToFeaturesConverter
- ReadsToFeaturesDatasetConverter
- ReadsToFragmentsConverter
- ReadsToFragmentsDatasetConverter
- ReadsToGenotypesConverter
- ReadsToGenotypesDatasetConverter
- ReadsToReadsConverter
- ReadsToSequencesConverter
- ReadsToSequencesDatasetConverter
- ReadsToSlicesConverter
- ReadsToSlicesDatasetConverter
- ReadsToVariantContextsConverter
- ReadsToVariantsConverter
- ReadsToVariantsDatasetConverter
- SequencesToAlignmentsConverter
- SequencesToAlignmentsDatasetConverter
- SequencesToCoverageConverter
- SequencesToCoverageDatasetConverter
- SequencesToFeaturesConverter
- SequencesToFeaturesDatasetConverter
- SequencesToFragmentsConverter
- SequencesToFragmentsDatasetConverter
- SequencesToGenotypesConverter
- SequencesToGenotypesDatasetConverter
- SequencesToReadsConverter
- SequencesToReadsDatasetConverter
- SequencesToSequencesConverter
- SequencesToSlicesConverter
- SequencesToSlicesDatasetConverter
- SequencesToVariantContextsConverter
- SequencesToVariantsConverter
- SequencesToVariantsDatasetConverter
- SlicesToAlignmentsConverter
- SlicesToAlignmentsDatasetConverter
- SlicesToCoverageConverter
- SlicesToCoverageDatasetConverter
- SlicesToFeaturesConverter
- SlicesToFeaturesDatasetConverter
- SlicesToFragmentsConverter
- SlicesToFragmentsDatasetConverter
- SlicesToGenotypesConverter
- SlicesToGenotypesDatasetConverter
- SlicesToReadsConverter
- SlicesToReadsDatasetConverter
- SlicesToSequencesConverter
- SlicesToSequencesDatasetConverter
- SlicesToSlicesConverter
- SlicesToVariantContextsConverter
- SlicesToVariantsConverter
- SlicesToVariantsDatasetConverter
- ToAlignmentDatasetConversion
- ToCoverageDatasetConversion
- ToFeatureDatasetConversion
- ToFragmentDatasetConversion
- ToGenotypeDatasetConversion
- ToReadDatasetConversion
- ToSequenceDatasetConversion
- ToSliceDatasetConversion
- ToVariantContextDatasetConversion
- ToVariantDatasetConversion
- VariantContextsToAlignmentsConverter
- VariantContextsToCoverageConverter
- VariantContextsToFeaturesConverter
- VariantContextsToFragmentsConverter
- VariantContextsToGenotypesConverter
- VariantContextsToReadsConverter
- VariantContextsToSequencesConverter
- VariantContextsToSlicesConverter
- VariantContextsToVariantContextConverter
- VariantContextsToVariantsConverter
- VariantsToAlignmentsConverter
- VariantsToAlignmentsDatasetConverter
- VariantsToCoverageConverter
- VariantsToCoverageDatasetConverter
- VariantsToFeaturesConverter
- VariantsToFeaturesDatasetConverter
- VariantsToFragmentsConverter
- VariantsToFragmentsDatasetConverter
- VariantsToGenotypesConverter
- VariantsToGenotypesDatasetConverter
- VariantsToReadsConverter
- VariantsToReadsDatasetConverter
- VariantsToSequencesConverter
- VariantsToSequencesDatasetConverter
- VariantsToSlicesConverter
- VariantsToSlicesDatasetConverter
- VariantsToVariantContextConverter
- VariantsToVariantsConverter

c

org.bdgenomics.adam.api.java

# AlignmentsToVariantsDatasetConverter 

###

#### final class AlignmentsToVariantsDatasetConverter extends ToVariantDatasetConversion[Alignment, Alignment, AlignmentDataset]

Linear Supertypes
ToVariantDatasetConversion[Alignment, Alignment, AlignmentDataset], GenomicDatasetConversion[Alignment, Alignment, AlignmentDataset, Variant, Variant, VariantDataset], Function2[AlignmentDataset, Dataset[Variant], VariantDataset], Serializable, AnyRef, Any
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Ordering

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2. By Inheritance

Inherited

1. AlignmentsToVariantsDatasetConverter
2. ToVariantDatasetConversion
3. GenomicDatasetConversion
4. Function2
5. Serializable
6. AnyRef
7. Any

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Visibility

1. Public
2. All

### Instance Constructors

1.  new AlignmentsToVariantsDatasetConverter()

### 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 call(v1: AlignmentDataset, v2: Dataset[Variant]): VariantDataset
   Definition Classes
     AlignmentsToVariantsDatasetConverter → GenomicDatasetConversion → Function2
6.  def clone(): AnyRef
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native()
7.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
8.  def equals(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
9.  def finalize(): Unit
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] )
10.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
11.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
12.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
13.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
14.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
15.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
16.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
17.  def toString(): String
    Definition Classes
      AnyRef → Any
18.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
19.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
20.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
21.  val yTag: scala.reflect.api.JavaUniverse.TypeTag[Variant]
    Definition Classes
      ToVariantDatasetConversion → GenomicDatasetConversion

### Inherited from ToVariantDatasetConversion[Alignment, Alignment, AlignmentDataset]

### Inherited from GenomicDatasetConversion[Alignment, Alignment, AlignmentDataset, Variant, Variant, VariantDataset]

### Inherited from Function2[AlignmentDataset, Dataset[Variant], VariantDataset]

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped