htsjdk.variant.variantcontext.writer

Class BCF2FieldWriterManager

java.lang.Object

htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager

public class BCF2FieldWriterManager
extends java.lang.Object

See #BCFWriter for documentation on this classes role in encoding BCF2 files

Since:

06/12

Constructor Summary

Constructors

Constructor and Description
BCF2FieldWriterManager()

Method Summary

Methods

Modifier and Type	Method and Description
BCF2FieldWriter.GenotypesWriter	getGenotypeFieldWriter(java.lang.String field) Get a genotypes writer specialized to encode values for genotypes field
BCF2FieldWriter.SiteWriter	getSiteFieldWriter(java.lang.String field) Get a site writer specialized to encode values for site info field
<T> T	getWriter(java.lang.String key, java.util.Map<java.lang.String,T> map)
void	setup(VCFHeader header, BCF2Encoder encoder, java.util.Map<java.lang.String,java.lang.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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BCF2FieldWriterManager

public BCF2FieldWriterManager()

Method Detail

setup

public void setup(VCFHeader header,
         BCF2Encoder encoder,
         java.util.Map<java.lang.String,java.lang.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(java.lang.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(java.lang.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(java.lang.String key,
              java.util.Map<java.lang.String,T> map)