public class AnnotatedVCFWriter extends Object implements Closeable
VariantContext and write out through HTSJDK (i.e. in VCF/BCF format).| Constructor and Description |
|---|
AnnotatedVCFWriter(ReferenceDictionary refDict,
htsjdk.variant.vcf.VCFHeader vcfHeader,
com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap,
String vcfPath,
JannovarAnnotateVCFOptions options,
com.google.common.collect.ImmutableList<String> args) |
| Modifier and Type | Method and Description |
|---|---|
void |
close()
Close VariantContextWriter in out.
|
htsjdk.variant.vcf.VCFHeader |
getVCFHeader() |
void |
put(htsjdk.variant.variantcontext.VariantContext vc) |
public AnnotatedVCFWriter(ReferenceDictionary refDict, htsjdk.variant.vcf.VCFHeader vcfHeader, com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap, String vcfPath, JannovarAnnotateVCFOptions options, com.google.common.collect.ImmutableList<String> args)
public htsjdk.variant.vcf.VCFHeader getVCFHeader()
VCFHeader that is usedpublic void put(htsjdk.variant.variantcontext.VariantContext vc)
public void close()
close in interface Closeableclose in interface AutoCloseableCopyright © 2016. All rights reserved.