ADAM_2.12: Core 0.35.0 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 algorithms
  Definition Classes
    adam
-  package converters
  Definition Classes
    adam
- AlignmentConverter
- DefaultHeaderLines
- VariantContextConverter
-  package ds
  Definition Classes
    adam
-  package io
  Definition Classes
    adam
-  package models
  Definition Classes
    adam
-  package projections
  Definition Classes
    adam
-  package rich
  Definition Classes
    adam
-  package serialization
  Definition Classes
    adam
-  package sql
  Definition Classes
    adam
-  package util
  Definition Classes
    adam

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org.bdgenomics.adam

# converters 

#### package converters

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Ordering

1. Alphabetic

Visibility

1. Public
2. All

### Type Members

1.  class AlignmentConverter extends Serializable with Logging

   Conversions between Alignments and other formats.

2.  class VariantContextConverter extends Serializable with Logging

   This class converts VCF data to and from ADAM.

   This class converts VCF data to and from ADAM. This translation occurs at the abstraction level of the htsjdk VariantContext which represents VCF data, and at the ADAMVariantContext level, which aggregates ADAM variant/genotype/annotation data together.

   If a genotype annotation has a corresponding set of fields in the VCF standard, a conversion to/from the htsjdk VariantContext should be implemented in this class.

### Value Members

1.  object AlignmentConverter extends Serializable

   Singleton object to assist with converting Alignments.

   Singleton object to assist with converting Alignments.

   Singleton object exists due to cross reference from org.bdgenomics.adam.rdd.read.AlignmentDatasetFunctions.

2.  object DefaultHeaderLines

   Default set of VCF header lines for INFO and GT format fields supported in ADAM.

3.  object VariantContextConverter extends Serializable

   Object for converting between htsjdk and ADAM VariantContexts.

   Object for converting between htsjdk and ADAM VariantContexts.

   Handles Variant, Genotype, Allele, and various genotype annotation conversions. Does not handle Variant annotations. Genotype annotations are annotations in the VCF GT field while Variant annotations are annotations contained in the VCF INFO field.

### Ungrouped