getToolkit().getArguments().variant_index_parameter != OPTIMAL_GVCF_INDEX_PARAMETER) {
throw new UserException.GVCFIndexException(OPTIMAL_GVCF_INDEX_TYPE, OPTIMAL_GVCF_INDEX_PARAMETER);
}
try {
vcfWriter = new GVCFWriter(vcfWriter, GVCFGQBands,SCAC.genotypeArgs.samplePloidy);
} catch ( IllegalArgumentException e ) {
throw new UserException.BadArgumentValue("GQBands", "are malformed: " + e.getMessage());
}
}
}