org.bdgenomics.adam

# converters

#### package converters

Visibility

1. Public
2. All

### Type Members

1. #### class AlignmentConverter extends Serializable

   This class contains methods to convert Alignments to 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 DefaultHeaderLines

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

2. #### 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