Method getValidGtStr

src/main/java/com/rtg/vcf/VcfUtils.java:770–779

Get the string 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, or the sample is invalid.

(VcfRecord rec, int sample)

   * @throws NoTalkbackSlimException if the record does not contain GT values, or the sample is invalid.
   */
  public static String getValidGtStr(VcfRecord rec, int sample) {
    final List<String> gtList = rec.getFormat(FORMAT_GENOTYPE);
    if (gtList == null) {
      throw new VcfFormatException("VCF record does not contain GT field, record: " + rec.toString());
    }
    if (sample >= gtList.size()) {
      throw new VcfFormatException("Invalid sample number " + sample + ", record: " + rec.toString());
    }
    return gtList.get(sample);
  }

  /**
   * Check if the record contains a well-defined variant genotype for the specified sample.