int extractRead(Idx2BWT * idx2BWT, unsigned long long readID, char* seq, char* qual)
{
static char dnaChars[] = {'A','C','G','T'};
int readLen = 0;
BWT *bwt = idx2BWT->bwt;
ULL l = idx2BWT->bwt->cumulativeFreq[4] + readID;
for (;;) {
unsigned int c = _getBWTvalue(idx2BWT->bwt, l);
if (c == 4) {
for (int i = 0, j = readLen - 1; i < j; ++i, --j) {
seq[i] ^= seq[j];
seq[j] ^= seq[i];
seq[i] ^= seq[j];
}
seq[readLen] = 0;
l = bwt->cumulativeFreq[c] + BWTOccValue(bwt, l, c);
fprintf(stderr, "ReadID verify: %d. Just for debug, comment this at file %s, line: %d.\n", idx2BWT->readIDtable[l - bwt->cumulativeFreq[4]], __FILE__, __LINE__);
return readLen;
} else {
l = bwt->cumulativeFreq[c] + BWTOccValue(bwt, l, c);
seq[readLen] = dnaChars[c];
++readLen;
}
}
}
//给出saIndex, foreward 算出 saIndex
void BWTSARangeForeward(Idx2BWT * idx2BWT, const unsigned char c,
unsigned int *saIndexLeft, unsigned int *saIndexRight) {
BWT * rev_bwt = idx2BWT->rev_bwt;
BWT *bwt = idx2BWT->bwt;
unsigned int l = (*saIndexLeft);
unsigned int r = (*saIndexRight);
(*saIndexLeft) = bwt->cumulativeFreq[c] + BWTOccValue(rev_bwt, l, c) + 1;
(*saIndexRight) = bwt->cumulativeFreq[c] + BWTOccValue(rev_bwt, r + 1, c);
}
int _dfsExtractReadInf(Idx2BWT * idx2BWT, ULL saL, ULL saR, ReadInf* &ri, int outputLimit, int strand, int _pos)
{
ULL l, r;
unsigned int c;
ULL numSAs = 0;
int totalCount = 0;
l = saL, r = saR;
if (saL == saR) { // only one route, backward search to the end
do {
c = _getBWTvalue(idx2BWT->bwt, saL);
saL = idx2BWT->bwt->cumulativeFreq[c] + BWTOccValue(idx2BWT->bwt, saL, c);
++_pos;
} while (c != 4);
ri->read_id = idx2BWT->readIDtable[saL - idx2BWT->bwt->cumulativeFreq[4]];
ri->strand = strand;
ri->pos = _pos - 1;
++ri;
return 1;
}
for (int i = 0; i < 4; ++i) { // try A C G T
BWTSARangeBackward(idx2BWT, i ,&saL, &saR);
if (saL <= saR && saR-saL <= r-l) {
int outputCount = _dfsExtractReadInf(idx2BWT, saL, saR, ri, outputLimit, strand, _pos + 1);
outputLimit -= outputCount;
totalCount += outputCount;
if (outputLimit <= 0) return totalCount;
numSAs += saR - saL + 1;
if (numSAs == r - l + 1) { // no branch at all
return totalCount;
}
}
saL = l; saR = r; // reset ranges
}
// try add $
BWTSARangeBackward(idx2BWT, 4 ,&saL, &saR); // 4 is $
if (saL <= saR) {
int limit = saR - saL + 1;
if (limit > outputLimit) {
limit = outputLimit;
}
for (int i = 0; i < limit; ++i) {
ri->read_id = idx2BWT->readIDtable[saL + i - idx2BWT->bwt->cumulativeFreq[4]];
ri->strand = strand;
ri->pos = _pos;
++ri;
}
totalCount += limit;
}
return totalCount;
}
