public class AnnotatedJannovarWriter extends AnnotatedVariantWriter
VariantContext
and write out in Jannovar format.Constructor and Description |
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AnnotatedJannovarWriter(ReferenceDictionary refDict,
com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap,
String vcfPath,
JannovarOptions options) |
Modifier and Type | Method and Description |
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void |
close()
Close writer, free resources
|
String |
getOutFileName()
Returns output path
|
void |
put(htsjdk.variant.variantcontext.VariantContext vc)
Write out record for VariantContext.
|
public AnnotatedJannovarWriter(ReferenceDictionary refDict, com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap, String vcfPath, JannovarOptions options) throws IOException
IOException
public String getOutFileName()
AnnotatedVariantWriter
getOutFileName
in class AnnotatedVariantWriter
public void close()
public void put(htsjdk.variant.variantcontext.VariantContext vc) throws AnnotationException, IOException
put
in class AnnotatedVariantWriter
AnnotationException
- when a problem with annotation occursIOException
- when problem with I/O occursCopyright © 2016. All rights reserved.