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VariantVcfDataWriter.getOriginalAlleles
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How to use
getOriginalAlleles
method
in
org.opencb.opencga.storage.core.variant.io.VariantVcfDataWriter

Best Java code snippets using org.opencb.opencga.storage.core.variant.io.VariantVcfDataWriter.getOriginalAlleles (Showing top 1 results out of 315)

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}
origin: opencb/opencga

List<String> originalAlleles = getOriginalAlleles(ori);
List<String> allelesArray;
if (originalAlleles != null) {
org.opencb.opencga.storage.core.variant.ioVariantVcfDataWritergetOriginalAlleles

Javadoc

Assumes that ori is in the form "POS:REF:ALT_0(,ALT_N)*:ALT_IDX". ALT_N is the n-th allele if this is the n-th variant resultant of a multiallelic vcf row

Popular methods of VariantVcfDataWriter

  • <init>
  • adjustedVariantStart
    Adjust start/end if a reference base is required due to an empty allele. All variants are checked du
  • buildAlleles
  • addAnnotationInfo
  • addAnnotations
  • addCohortInfo
  • addStats
  • buildAllele
  • close
  • convertVariantToVariantContext
    Convert org.opencb.biodata.models.variant.Variant into a htsjdk.variant.variantcontext.VariantContex
  • getOri
  • getOriginalAlleleIndex
  • getOri,
  • getOriginalAlleleIndex,
  • getReferenceBase,
  • getSamples,
  • htsExport,
  • open,
  • post,
  • pre,
  • vcfExport

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