Package htsjdk.variant.variantcontext.writer

Class BCF2FieldWriterManager

java.lang.Object
htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager
public class BCF2FieldWriterManager extends Object
See #BCFWriter for documentation on this classes role in encoding BCF2 files
Since:
06/12

  • Constructor Details

    • BCF2FieldWriterManager

      public BCF2FieldWriterManager()

  • Method Details

    • setup

      public void setup(VCFHeader header, BCF2Encoder encoder, Map<String,Integer> stringDictionary)
      Setup the FieldWriters appropriate to each INFO and FORMAT in the VCF header Must be called before any of the getter methods will work
      Parameters:
      header - a VCFHeader containing description for every INFO and FORMAT field we'll attempt to write out to BCF
      encoder - the encoder we are going to use to write out the BCF2 data
      stringDictionary - a map from VCFHeader strings to their offsets for encoding

    • getSiteFieldWriter

      public BCF2FieldWriter.SiteWriter getSiteFieldWriter(String field)
      Get a site writer specialized to encode values for site info field
      Parameters:
      field - key found in the VCF header INFO records
      Returns:
      non-null writer if one can be found, or null if none exists for field

    • getGenotypeFieldWriter

      public BCF2FieldWriter.GenotypesWriter getGenotypeFieldWriter(String field)
      Get a genotypes writer specialized to encode values for genotypes field
      Parameters:
      field - key found in the VCF header FORMAT records
      Returns:
      non-null writer if one can be found, or null if none exists for field

    • getWriter

      public <T> T getWriter(String key, Map<String,T> map)