Package htsjdk.variant.vcf
package htsjdk.variant.vcf
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ClassDescriptionA feature codec for the VCF3 specification, to read older VCF files.A class representing ALT fields in the VCF headerA feature codec for the VCF 4 specificationa base class for compound header lines, which include info lines and format lines (so far)A special class representing a contig VCF header line.Functions specific to encoding VCF records.Simplified interface for reading from VCF/BCF files.A class to represent a VCF headerthe count encodings we use for fields in VCF header linesA class for translating between vcf header versionsthe type encodings we use for fields in VCF header linesinformation that identifies each header versionan interface for ID-based header linesAn iterator of `VariantContext`.A Class building
VCFIterator
Example:A class representing META fields in the VCF headerA no-op implementation of VCFTextTransformer for pre-v43 VCFs, when such encodings are not supported and no transformation need be done.A class representing PEDIGREE fields in the VCF headerText transformer for attribute values embedded in VCF.Interface for reading VCF/BCF files.Writes VariantContext instances to an OutputStream without headers or metadata.A class representing SAMPLE fields in the VCF headerManages header lines for standard VCFInterface for transforming attribute values embedded in VCF.