htsjdk.samtools.BinaryCigarCodec Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools;
import java.nio.ByteBuffer;
/**
* Converter between disk and in-memory (object, not String) CIGAR representation.
*/
class BinaryCigarCodec {
/**
* Convert CIGAR from object representation to disk representation.
* @return Array of unsigned ints, one for each element of CIGAR.
*/
static int[] encode(final Cigar cigar) {
if (cigar.numCigarElements() == 0) {
return new int[0];
}
// Binary rep can be no longer than 1/2 of text rep
// Although this is documented as uint, I think lengths will never get that long,
// and it's a pain in Java.
final int[] binaryCigar = new int[cigar.numCigarElements()];
int binaryCigarLength = 0;
for (int i = 0; i < cigar.numCigarElements(); ++i) {
final CigarElement cigarElement = cigar.getCigarElement(i);
final int op = CigarOperator.enumToBinary(cigarElement.getOperator());
binaryCigar[binaryCigarLength++] = cigarElement.getLength() << 4 | op;
}
return binaryCigar;
}
/**
* Convert CIGAR from disk representation to object.
* @param binaryCigar ByteArray that is assumed to have byte order set appropriately for extracting ints.
*/
static Cigar decode(final ByteBuffer binaryCigar) {
final Cigar ret = new Cigar();
while (binaryCigar.hasRemaining()) {
final int cigarette = binaryCigar.getInt();
ret.add(binaryCigarToCigarElement(cigarette));
}
return ret;
}
/**
* Convert CIGAR from disk representation to object.
* @param binaryCigar Array of unsigned ints, one for each CIGAR element.
*/
static Cigar decode(final int[] binaryCigar) {
final Cigar ret = new Cigar();
for (final int cigarette : binaryCigar) {
ret.add(binaryCigarToCigarElement(cigarette));
}
return ret;
}
/**
* @param cigarette CIGAR element (operator + length) encoded as an unsigned int.
* @return Object representation of the CIGAR element.
*/
private static CigarElement binaryCigarToCigarElement(final int cigarette) {
final int binaryOp = cigarette & 0xf;
final int length = cigarette >>> 4;
return new CigarElement(length, CigarOperator.binaryToEnum(binaryOp));
}
}