How to use

buildAlleles

method

in

org.opencb.opencga.storage.core.variant.io.VariantVcfDataWriter

  allelesArray = originalAlleles;
} else {
  allelesArray = buildAlleles(variant, adjustedRange);

@Test
public void buildAlleles_SecAlt_INDEL() throws Exception {
  StudyConfiguration sc = new StudyConfiguration(1, "1");
  VariantVcfDataWriter dw = new VariantVcfDataWriter(sc, null, null, null);
  Variant variant = createVariantSecAlt("1:123:A:C", "1:122:GGT:-");
  List<String> alles = dw.buildAlleles(variant, new ImmutablePair<>(121, 124));
  assertEquals("Missing alleles", 3, alles.size());
  assertEquals("Ref allele not correctly adjusted", "NNAN", alles.get(0));
  assertEquals("Ref allele not correctly adjusted", "NNCN", alles.get(1));
  assertEquals("Ref allele not correctly adjusted", "N", alles.get(2));
}

@Test
public void buildAlleles_SecAlt_MNV() throws Exception {
  StudyConfiguration sc = new StudyConfiguration(1, "1");
  VariantVcfDataWriter dw = new VariantVcfDataWriter(sc, null, null, null);
  Variant variant = createVariantSecAlt("1:123:A:C", "1:122:GG:TT");
  List<String> alles = dw.buildAlleles(variant, new ImmutablePair<>(122, 123));
  assertEquals("Missing alleles", 3, alles.size());
  assertEquals("Ref allele not correctly adjusted", "NA", alles.get(0));
  assertEquals("Ref allele not correctly adjusted", "NC", alles.get(1));
  assertEquals("Ref allele not correctly adjusted", "TT", alles.get(2));
}