htsjdk.samtools.cram.build.Utils Maven / Gradle / Ivy
/**
* ****************************************************************************
* Copyright 2013 EMBL-EBI
*
* Licensed 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 htsjdk.samtools.cram.build;
final public class Utils {
private Utils() {};
/**
* CRAM operates with upper case bases, so both read and ref bases should be
* upper-cased and vocab controlled. This method does exactly this: upper
* case acgt and replace everything else with N.
*
* @param base a base to normalize
* @return a normalized base
*/
public static byte normalizeBase(final byte base) {
switch (base) {
case 'a':
case 'A':
return 'A';
case 'c':
case 'C':
return 'C';
case 'g':
case 'G':
return 'G';
case 't':
case 'T':
return 'T';
default:
return 'N';
}
}
}