htsjdk.variant.bcf2

Interface BCF2GenotypeFieldDecoders.Decoder

Enclosing class:

BCF2GenotypeFieldDecoders

public static interface BCF2GenotypeFieldDecoders.Decoder

Decoder a field (implicit from creation) encoded as typeDescriptor in the decoder object in the GenotypeBuilders one for each sample in order. The way this works is that this decode method iterates over the builders, decoding a genotype field in BCF2 for each sample from decoder. This system allows us to easily use specialized decoders for specific genotype field values. For example, we use a special decoder to directly read the BCF2 data for the PL field into a int[] rather than the generic List of Integer

Method Summary

Modifier and Type	Method and Description
void	decode(java.util.List<Allele> siteAlleles, java.lang.String field, BCF2Decoder decoder, byte typeDescriptor, int numElements, GenotypeBuilder[] gbs)

Method Detail

decode

void decode(java.util.List<Allele> siteAlleles,
            java.lang.String field,
            BCF2Decoder decoder,
            byte typeDescriptor,
            int numElements,
            GenotypeBuilder[] gbs)
     throws java.io.IOException

Throws:

java.io.IOException