public class BCF2FieldWriterManager extends Object
Constructor and Description |
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BCF2FieldWriterManager() |
Modifier and Type | Method and Description |
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BCF2FieldWriter.GenotypesWriter |
getGenotypeFieldWriter(String field)
Get a genotypes writer specialized to encode values for genotypes field
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BCF2FieldWriter.SiteWriter |
getSiteFieldWriter(String field)
Get a site writer specialized to encode values for site info field
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<T> T |
getWriter(String key,
Map<String,T> map) |
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
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public void setup(VCFHeader header, BCF2Encoder encoder, Map<String,Integer> stringDictionary)
header
- a VCFHeader containing description for every INFO and FORMAT field we'll attempt to write out to BCFencoder
- the encoder we are going to use to write out the BCF2 datastringDictionary
- a map from VCFHeader strings to their offsets for encodingpublic BCF2FieldWriter.SiteWriter getSiteFieldWriter(String field)
field
- key found in the VCF header INFO recordspublic BCF2FieldWriter.GenotypesWriter getGenotypeFieldWriter(String field)
field
- key found in the VCF header FORMAT records