package converters
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Type Members
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class
AlignmentConverter extends Serializable with Logging
Conversions between Alignments and other formats.
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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
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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.
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object
DefaultHeaderLines
Default set of VCF header lines for INFO and GT format fields supported in ADAM.
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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.