htsjdk.samtools.TextCigarCodec 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 htsjdk.samtools.util.StringUtil;
/**
* Convert between String and Cigar class representations of CIGAR.
*/
public class TextCigarCodec
{
private static final byte ZERO_BYTE = "0".getBytes()[0];
private static final byte NINE_BYTE = "9".getBytes()[0];
/**
* Convert from Cigar class representation to String.
* @param cigar in Cigar class format
* @return CIGAR in String form ala SAM text file. "*" means empty CIGAR.
*/
public static String encode(final Cigar cigar) {
if (cigar.isEmpty()) {
return SAMRecord.NO_ALIGNMENT_CIGAR;
}
final StringBuilder ret = new StringBuilder();
for (final CigarElement cigarElement : cigar.getCigarElements()) {
ret.append(cigarElement.getLength());
ret.append(cigarElement.getOperator());
}
return ret.toString();
}
/**
* Convert from String CIGAR representation to Cigar class representation. Does not
* do validation beyond the most basic CIGAR string well-formedness, i.e. each operator is
* valid, and preceded by a decimal length.
* @param textCigar CIGAR in String form ala SAM text file. "*" means empty CIGAR.
* @throws RuntimeException if textCigar is invalid at the most basic level.
* @return cigar in Cigar class format
*/
public static Cigar decode(final String textCigar) {
if (SAMRecord.NO_ALIGNMENT_CIGAR.equals(textCigar)) {
return new Cigar();
}
final Cigar ret = new Cigar();
final byte[] cigarBytes = StringUtil.stringToBytes(textCigar);
for (int i = 0; i < cigarBytes.length; ++i) {
if (!isDigit(cigarBytes[i])) {
throw new IllegalArgumentException("Malformed CIGAR string: " + textCigar);
}
int length = (cigarBytes[i] - ZERO_BYTE);
for (++i; isDigit(cigarBytes[i]); ++i) {
length = (length * 10) + cigarBytes[i] - ZERO_BYTE;
}
final CigarOperator operator = CigarOperator.characterToEnum(cigarBytes[i]);
ret.add(new CigarElement(length, operator));
}
return ret;
}
private static boolean isDigit(final byte c) {
return c >= ZERO_BYTE && c <= NINE_BYTE;
}
}
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