@Deprecated public class VcfStringAnnotatorTask extends Object implements org.opencb.commons.run.ParallelTaskRunner.TaskWithException<String,org.opencb.biodata.models.variant.Variant,Exception>
Modifier and Type | Class and Description |
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static class |
VcfStringAnnotatorTask.SharedContext
Deprecated.
|
Constructor and Description |
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VcfStringAnnotatorTask(htsjdk.variant.vcf.VCFHeader header,
htsjdk.variant.vcf.VCFHeaderVersion version,
List<VariantAnnotator> variantAnnotatorList,
VcfStringAnnotatorTask.SharedContext sharedContext)
Deprecated.
|
VcfStringAnnotatorTask(htsjdk.variant.vcf.VCFHeader header,
htsjdk.variant.vcf.VCFHeaderVersion version,
List<VariantAnnotator> variantAnnotatorList,
VcfStringAnnotatorTask.SharedContext sharedContext,
boolean normalize,
org.opencb.biodata.tools.variant.VariantNormalizer.VariantNormalizerConfig variantNormalizerConfig)
Deprecated.
|
Modifier and Type | Method and Description |
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List<org.opencb.biodata.models.variant.Variant> |
apply(List<String> batch)
Deprecated.
|
List<org.opencb.biodata.models.variant.Variant> |
drain()
Deprecated.
|
void |
post()
Deprecated.
|
void |
pre()
Deprecated.
|
public VcfStringAnnotatorTask(htsjdk.variant.vcf.VCFHeader header, htsjdk.variant.vcf.VCFHeaderVersion version, List<VariantAnnotator> variantAnnotatorList, VcfStringAnnotatorTask.SharedContext sharedContext)
public VcfStringAnnotatorTask(htsjdk.variant.vcf.VCFHeader header, htsjdk.variant.vcf.VCFHeaderVersion version, List<VariantAnnotator> variantAnnotatorList, VcfStringAnnotatorTask.SharedContext sharedContext, boolean normalize, org.opencb.biodata.tools.variant.VariantNormalizer.VariantNormalizerConfig variantNormalizerConfig)
public void pre()
pre
in interface org.opencb.commons.run.Task<String,org.opencb.biodata.models.variant.Variant>
public List<org.opencb.biodata.models.variant.Variant> apply(List<String> batch) throws Exception
public void post()
post
in interface org.opencb.commons.run.Task<String,org.opencb.biodata.models.variant.Variant>
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