Method getType

src/main/java/com/rtg/vcf/VariantType.java:130–160

Determine the type of variant given a genotype @param rec the VCF record containing the allele definitions @param gtSplit the genotype, as allele indices @return the type of variant

(VcfRecord rec, int[] gtSplit)

   * @return the type of variant
   */
  public static VariantType getType(VcfRecord rec, int[] gtSplit) {
    boolean allMissing = true;
    int altId = 0;
    int gtPos;
    for (gtPos = 0; gtPos < gtSplit.length; gtPos++) {
      final int a = gtSplit[gtPos];
      if (a != -1) {
        allMissing = false;
        if (a != 0) {
          altId = a;
          gtPos++;
          break;
        }
      }
    }
    if (allMissing) {
      return VariantType.NO_CALL;
    }
    if (altId == 0) {
      return VariantType.UNCHANGED;
    }
    final String[] alleles = VcfUtils.getAlleleStrings(rec);
    VariantType altType = getType(alleles[0], alleles[altId]);
    for (; gtPos < gtSplit.length; gtPos++) {
      final int a = gtSplit[gtPos];
      if (a > 0 && a != altId) {
        altType = getPrecedence(altType, getType(alleles[0], alleles[a]));
      }
    }
    return altType;
  }

  /**
   * Determine the type of variant given a reference allele and a called/alternative allele.