Method isValidGt

src/main/java/com/rtg/vcf/VcfUtils.java:294–302

Check whether the split GT array references valid allele IDs @param rec the record containing ref and alt alleles @param gt the split GT. @return false if any of the GT elements are out of range.

(VcfRecord rec, int[] gt)

   * @return false if any of the GT elements are out of range.
   */
  public static boolean isValidGt(VcfRecord rec, int[] gt) {
    final int maxId = rec.getAltCalls().size();
    for (int gtId : gt) {
      if (gtId < MISSING_GT || gtId > maxId) {
        return false;
      }
    }
    return true;
  }

  /**
   * Check if the supplied file is has an extension indicative of VCF.