--bowtie-chunkmbs

[rsem.git] / SingleQModel.h

diff --git a/SingleQModel.h b/SingleQModel.h
index dff9c4691153911a3d060b9d063a4856f4628b77..5d4191a809d39c454e1bfea7805b12f5fde990c0 100644 (file)
--- a/SingleQModel.h
+++ b/SingleQModel.h
@@ -283,9 +283,12 @@ void SingleQModel::estimateFromReads(const char* readFN) {
 
                        int cnt = 0;
                        while (reader.next(read)) {
-                               mld != NULL ? mld->update(read.getReadLength(), 1.0) : gld->update(read.getReadLength(), 1.0);
-                               qd->update(read.getQScore());
-                               if (i == 0) { nqpro->updateC(read.getReadSeq(), read.getQScore()); }
+                               if (!read.isLowQuality()) {
+                                 mld != NULL ? mld->update(read.getReadLength(), 1.0) : gld->update(read.getReadLength(), 1.0);
+                                 qd->update(read.getQScore());
+                                 if (i == 0) { nqpro->updateC(read.getReadSeq(), read.getQScore()); }
+                               }
+                               else if (verbose && read.getReadLength() < OLEN) { printf("Warning: Read %s is ignored due to read length < %d!\n", read.getName().c_str(), OLEN); }
 
                                ++cnt;
                                if (verbose && cnt % 1000000 == 0) { printf("%d READS PROCESSED\n", cnt); }
@@ -334,12 +337,12 @@ void SingleQModel::read(const char* inpF) {
        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);
        gld->read(fi);
-       fscanf(fi, "%d", &val);
+       assert(fscanf(fi, "%d", &val) == 1);
        if (val > 0) {
                if (mld == NULL) mld = new LenDist();
                mld->read(fi);
@@ -349,15 +352,18 @@ void SingleQModel::read(const char* inpF) {
        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 SingleQModel::write(const char* outF) {
        FILE *fo = fopen(outF, "w");
 
@@ -440,9 +446,8 @@ bool SingleQModel::simulate(int rid, SingleReadQ& read, int& sid) {
                }
        }
 
-       std::ostringstream stdout;
-       stdout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos;
-       name = stdout.str();
+       strout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos;
+       name = strout.str();
 
        read = SingleReadQ(name, readseq, qual);