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

Go to download

Show more of this group Show more artifacts with this name
Show all versions of convert Show documentation

Conversions to and from 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 ConversionStrategy to ValidationStrategy.
 */
final class ConversionStringencyToValidationStringency extends AbstractConverter {

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

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