void parseIt(SamParser *parser) {
// record_val & record_read are copies of val & read for record purpose
int val, record_val;
ReadType read, record_read;
HitType hit;
HitContainer<HitType> hits;
nHits = 0;
nUnique = nMulti = nIsoMulti = 0;
memset(N, 0, sizeof(N));
READ_INT_TYPE cnt = 0;
record_val = -2; //indicate no recorded read now
while ((val = parser->parseNext(read, hit)) >= 0) {
if (val >= 0 && val <= 2) {
// flush out previous read's info if needed
if (record_val >= 0) {
record_read.write(n_os, cat[record_val]);
++N[record_val];
}
// flush out previous read's hits if the read is alignable reads
if (record_val == 1) {
hits.updateRI();
nHits += hits.getNHits();
nMulti += hits.calcNumGeneMultiReads(gi);
nIsoMulti += hits.calcNumIsoformMultiReads();
hits.write(hit_out);
iter = counter.find(hits.getNHits());
if (iter != counter.end()) {
iter->second++;
}
else {
counter[hits.getNHits()] = 1;
}
}
hits.clear();
record_val = val;
record_read = read; // no pointer, thus safe
}
if (val == 1 || val == 5) {
hits.push_back(hit);
}
++cnt;
if (verbose && (cnt % 1000000 == 0)) { cout<< "Parsed "<< cnt<< " entries"<< endl; }
}
if (record_val >= 0) {
record_read.write(n_os, cat[record_val]);
++N[record_val];
}
if (record_val == 1) {
hits.updateRI();
nHits += hits.getNHits();
nMulti += hits.calcNumGeneMultiReads(gi);
nIsoMulti += hits.calcNumIsoformMultiReads();
hits.write(hit_out);
iter = counter.find(hits.getNHits());
if (iter != counter.end()) {
iter->second++;
}
else {
counter[hits.getNHits()] = 1;
}
}
nUnique = N[1] - nMulti;
}
