org.bdgenomics.convert.htsjdk.ValidationStringencyToConversionStringency Maven / Gradle / Ivy

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Conversions between HTSJDK and Big Data Genomics Avro Formats

There is a newer version: 1.0

/**
 * Licensed to Big Data Genomics (BDG) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The BDG licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package org.bdgenomics.convert.htsjdk;

import htsjdk.samtools.ValidationStringency;

import org.bdgenomics.convert.AbstractConverter;
import org.bdgenomics.convert.ConversionException;
import org.bdgenomics.convert.ConversionStringency;

import org.slf4j.Logger;

/**
 * Convert ValidationStrategy to ConversionStrategy.
 */
final class ValidationStringencyToConversionStringency extends AbstractConverter {

    /**
     * Package private constructor.
     */
    ValidationStringencyToConversionStringency() {
        super(ValidationStringency.class, ConversionStringency.class);
    }

    @Override
    public ConversionStringency convert(final ValidationStringency validationStringency,
                                        final ConversionStringency stringency,
                                        final Logger logger) throws ConversionException {
        if (validationStringency == null) {
            warnOrThrow(validationStringency, "must not be null", null, stringency, logger);
            return null;
        }
        if (validationStringency == ValidationStringency.SILENT) {
            return ConversionStringency.SILENT;
        }
        else if (validationStringency == ValidationStringency.LENIENT) {
            return ConversionStringency.LENIENT;
        }
        return ConversionStringency.STRICT;
    }
}