Method getValidGt

src/main/java/com/rtg/vcf/VcfUtils.java:755–761

Get the split GT for a sample, with validation checking @param rec record to extract the GT from @param sample the sample index @return the split GT field @throws NoTalkbackSlimException if the record does not contain GT values, the sample is invalid, or the GT itself is invalid.

(VcfRecord rec, int sample)

   * @throws NoTalkbackSlimException if the record does not contain GT values, the sample is invalid, or the GT itself is invalid.
   */
  public static int[] getValidGt(VcfRecord rec, int sample) {
    final int[] gtArr = splitGt(getValidGtStr(rec, sample));
    if (!isValidGt(rec, gtArr)) {
      throw new VcfFormatException("VCF record GT contains allele ID out of range, record: " + rec.toString());
    }
    return gtArr;
  }

  /**
   * Get the string GT for a sample, with validation checking