mw = NULL;
if (isMaster) {
- ori = new Orientation(params.probF);
if (!estRSPD) rspd = new RSPD(estRSPD);
qd = new QualDist();
mld = new LenDist(params.mate_minL, params.mate_maxL);
}
+ ori = new Orientation(params.probF);
gld = new LenDist(params.minL, params.maxL);
if (estRSPD) rspd = new RSPD(estRSPD, params.B);
qpro = new QProfile();
}
int getModelType() const { return model_type; }
-
- bool simulate(int, PairedEndReadQ&, SingleReadQ&, int&);
private:
static const int model_type = 3;
SingleReadQ mate1 = read.getMate1();
SingleReadQ mate2 = read.getMate2();
- mld->update(mate1.getReadLength(), 1.0);
- mld->update(mate2.getReadLength(), 1.0);
-
- qd->update(mate1.getQScore());
- qd->update(mate2.getQScore());
-
- if (i == 0) {
- nqpro->updateC(mate1.getReadSeq(), mate1.getQScore());
- nqpro->updateC(mate2.getReadSeq(), mate2.getQScore());
- }
+ if (!read.isLowQuality()) {
+ mld->update(mate1.getReadLength(), 1.0);
+ mld->update(mate2.getReadLength(), 1.0);
+
+ qd->update(mate1.getQScore());
+ qd->update(mate2.getQScore());
+
+ if (i == 0) {
+ nqpro->updateC(mate1.getReadSeq(), mate1.getQScore());
+ nqpro->updateC(mate2.getReadSeq(), mate2.getQScore());
+ }
+ }
+ else if (verbose && (mate1.getReadLength() < OLEN || mate2.getReadLength() < OLEN)) {
+ printf("Warning: Read %s is ignored due to at least one of the mates' length < %d!\n", read.getName().c_str(), OLEN);
+ }
++cnt;
if (verbose && cnt % 1000000 == 0) { printf("%d READS PROCESSED\n", cnt); }
FILE *fi = fopen(inpF, "r");
if (fi == NULL) { fprintf(stderr, "Cannot open %s! It may not exist.\n", inpF); exit(-1); }
- fscanf(fi, "%d", &val);
+ assert(fscanf(fi, "%d", &val) == 1);
assert(val == model_type);
ori->read(fi);
qpro->read(fi);
nqpro->read(fi);
- if (fscanf(fi, "%d", &M) == 1) {
- mw = new double[M + 1];
- for (int i = 0; i <= M; i++) fscanf(fi, "%lf", &mw[i]);
+ if (fscanf(fi, "%d", &val) == 1) {
+ if (M == 0) M = val;
+ if (M == val) {
+ mw = new double[M + 1];
+ for (int i = 0; i <= M; i++) assert(fscanf(fi, "%lf", &mw[i]) == 1);
+ }
}
+
fclose(fi);
}
-//Only master node can call
+//Only master node can call. Only be called at EM.cpp
void PairedEndQModel::write(const char* outF) {
FILE *fo = fopen(outF, "w");
readseq2 = qpro->simulate(sampler, mateL2, m2pos, m2dir, qual2, ref);
}
- std::ostringstream stdout;
- stdout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos<<"_"<<insertL;
- name = stdout.str();
+ strout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos<<"_"<<insertL;
+ name = strout.str();
read = PairedEndReadQ(SingleReadQ(name + "/1", readseq1, qual1), SingleReadQ(name + "/2", readseq2, qual2));