/**
* Create random read qualities
*
* @param length the length of the read
* @param allowNs whether or not to allow N's in the read
* @return an array with randomized bases (A-N) with equal probability
*/
public static byte[] createRandomReadBases(int length, boolean allowNs) {
Random random = GenomeAnalysisEngine.getRandomGenerator();
int numberOfBases = allowNs ? 5 : 4;
byte[] bases = new byte[length];
for (int i = 0; i < length; i++) {
switch (random.nextInt(numberOfBases)) {
case 0:
bases[i] = 'A';
break;
case 1:
bases[i] = 'C';
break;
case 2:
bases[i] = 'G';
break;
case 3:
bases[i] = 'T';
break;
case 4:
bases[i] = 'N';
break;
default:
throw new ReviewedStingException("Something went wrong, this is just impossible");
}
}
return bases;
}
/**
* Create random read qualities
*
* @param length the length of the read
* @return an array with randomized base qualities between 0 and 50
*/
public static byte[] createRandomReadQuals(int length) {
Random random = GenomeAnalysisEngine.getRandomGenerator();
byte[] quals = new byte[length];
for (int i = 0; i < length; i++) quals[i] = (byte) random.nextInt(50);
return quals;
}