const ReadInfo ReadInfoTable::getReadInfo(size_t idx) const
{
ReadInfo ri(getReadID(idx), getReadLength(idx));
return ri;
}
// pull out the bases that aren't clipped out
void AlignedRead::getUnclippedBases()
{
int readLen = getReadLength();
readBases = new byte[readLen];
readBasesLen = readLen;
baseQuals = new byte[readLen];
baseQualsLen = readLen;
const char *actualReadBases = read->AlignedBases.c_str();//read.getReadBases();
const char *actualBaseQuals = read->Qualities.c_str();//read.getBaseQualities();
int fromIndex = 0, toIndex = 0;
int qualD = 0;
//cout << CigarToString(read->CigarData) << endl;
for(Cigar::iterator itr = read->CigarData.begin(); itr != read->CigarData.end(); itr++) {
CigarOp ce = *itr;
int elementLength = ce.Length; //ce.getLength();
switch(ce.Type) {
case 'D':
fromIndex += elementLength;
qualD += elementLength;
break;
case 'S':
qualD -= elementLength;
break;
case 'M':
case 'I':
//System.arraycopy(actualReadBases, fromIndex, readBases, toIndex, elementLength);
for(int i = 0; i < elementLength; i++) {
readBases[toIndex + i] = actualReadBases[fromIndex + i];
}
//System.arraycopy(actualBaseQuals, fromIndex, baseQuals, toIndex, elementLength);
for(int i = 0; i < elementLength; i++) {
baseQuals[toIndex + i] = actualBaseQuals[fromIndex + i - qualD] - 33; //CONVERT FROM FASTQ TO PHRED
}
fromIndex += elementLength;
toIndex += elementLength;
break;
default:
break;
}
}
// cout << "###\t" << toIndex << endl;
// if we got clipped, trim the array
if(fromIndex != toIndex) {
char *trimmedRB = new char[toIndex];
char *trimmedBQ = new char[toIndex];
//System.arraycopy(readBases, 0, trimmedRB, 0, toIndex);
for(int i = 0; i < toIndex; i++) {
trimmedRB[i] = readBases[i];
}
//System.arraycopy(baseQuals, 0, trimmedBQ, 0, toIndex);
for(int i = 0; i < toIndex; i++) {
trimmedBQ[i] = baseQuals[i];
}
delete[] readBases;
delete[] baseQuals;
readBases = trimmedRB;
readBasesLen = toIndex;
baseQuals = trimmedBQ;
baseQualsLen = toIndex;
}
readBasesLen = toIndex;
}
