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.VCFHeader vcfHeader,
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.
|
String |
getOutFileName()
Create and return output file name.
|
htsjdk.variant.vcf.VCFHeader |
getVCFHeader() |
void |
put(htsjdk.variant.variantcontext.VariantContext vc)
Write out the given VariantContext with additional annotation.
|
public AnnotatedVCFWriter(ReferenceDictionary refDict, htsjdk.variant.vcf.VCFHeader vcfHeader, com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap, String vcfPath, JannovarOptions options, com.google.common.collect.ImmutableList<String> args)
public htsjdk.variant.vcf.VCFHeader getVCFHeader()
VCFHeader
that is usedpublic 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()
close
in interface Closeable
close
in interface AutoCloseable
close
in class AnnotatedVariantWriter
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