public class AnnotatedVCFWriter extends AnnotatedVariantWriter
VariantContext
and write out through HTSJDK (i.e. in VCF/BCF format).Constructor and Description |
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AnnotatedVCFWriter(ReferenceDictionary refDict,
htsjdk.variant.vcf.VCFFileReader reader,
com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap,
String vcfPath,
JannovarOptions options,
com.google.common.collect.ImmutableList<String> args) |
Modifier and Type | Method and Description |
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void |
close()
Close VariantContextWriter in out.
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String |
getOutFileName()
Create and return output file name.
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void |
put(htsjdk.variant.variantcontext.VariantContext vc)
Write out the given VariantContext with additional annotation.
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public AnnotatedVCFWriter(ReferenceDictionary refDict, htsjdk.variant.vcf.VCFFileReader reader, com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap, String vcfPath, JannovarOptions options, com.google.common.collect.ImmutableList<String> args)
public String getOutFileName()
options.outVCFFolder
is set then the file is written to this folder.getOutFileName
in class AnnotatedVariantWriter
public void put(htsjdk.variant.variantcontext.VariantContext vc)
AnnotatedVariantWriter
put
in class AnnotatedVariantWriter
public void close()
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