Package org.broadinstitute.gatk.utils.gvcf

Examples of org.broadinstitute.gatk.utils.gvcf.GVCFWriter


                        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());
                }
            }
        }
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