79 lines
2.6 KiB
Java
79 lines
2.6 KiB
Java
|
/*
|
||
|
|
The Broad Institute
|
||
|
|
SOFTWARE COPYRIGHT NOTICE AGREEMENT
|
||
|
|
This software and its documentation are copyright 2009 by the
|
||
|
|
Broad Institute/Massachusetts Institute of Technology. All rights are
|
||
|
|
reserved.
|
||
|
|
|
||
|
|
This software is supplied without any warranty or guaranteed support
|
||
|
|
whatsoever. Neither the Broad Institute nor MIT can be responsible for its
|
||
|
|
use, misuse, or functionality.
|
||
|
|
*/
|
||
|
|
package edu.mit.broad.sam;
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Convert between string and internal CIGAR representations
|
||
|
|
*/
|
||
|
|
public class TextCigarCodec
|
||
|
|
{
|
||
|
|
private static final byte ZERO_BYTE = "0".getBytes()[0];
|
||
|
|
private static final byte NINE_BYTE = "9".getBytes()[0];
|
||
|
|
|
||
|
|
private static final TextCigarCodec singleton = new TextCigarCodec();
|
||
|
|
|
||
|
|
/**
|
||
|
|
* It is not necssary to get the singleton but it is preferrable to use the same one
|
||
|
|
* over and over vs. creating a new object for each BAMRecord.
|
||
|
|
*/
|
||
|
|
static TextCigarCodec getSingleton() {
|
||
|
|
return singleton;
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Convert from interal CIGAR representation to String
|
||
|
|
*/
|
||
|
|
String encode(final Cigar cigar) {
|
||
|
|
if (cigar.numCigarElements() == 0) {
|
||
|
|
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();
|
||
|
|
}
|
||
|
|
|
||
|
|
Cigar decode(final String textCigar) {
|
||
|
|
if (SAMRecord.NO_ALIGNMENT_CIGAR.equals(textCigar)) {
|
||
|
|
return new Cigar();
|
||
|
|
}
|
||
|
|
final Cigar ret = new Cigar();
|
||
|
|
final byte[] cigarBytes = textCigar.getBytes();
|
||
|
|
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 boolean isDigit(final byte c) {
|
||
|
|
return c >= ZERO_BYTE && c <= NINE_BYTE;
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
}
|
||
|
|
|
||
|
|
/******************************************************************/
|
||
|
|
/**************************[END OF TextCigarCodec.java]*************************/
|
||
|
|
/******************************************************************/
|