--bowtie-chunkmbs

[rsem.git] / SingleModel.h

diff --git a/SingleModel.h b/SingleModel.h
index 532f79cd2c126c79199b1072508642394e083445..97ffd29c8ce9b7d499d99979bf0d51546cb17ab7 100644 (file)
--- a/SingleModel.h
+++ b/SingleModel.h
@@ -61,7 +61,6 @@ public:
                mw = NULL;
 
                if (isMaster) {
-                       ori = new Orientation(params.probF);
                        gld = new LenDist(params.minL, params.maxL);
                        if (mean >= EPSILON) {
                                mld = new LenDist(params.mate_minL, params.mate_maxL);
@@ -69,6 +68,7 @@ public:
                        if (!estRSPD) { rspd = new RSPD(estRSPD); }
                }
 
+               ori = new Orientation(params.probF);
                if (estRSPD) { rspd = new RSPD(estRSPD, params.B); }
                pro = new Profile(params.maxL);
                npro = new NoiseProfile();
@@ -273,8 +273,11 @@ void SingleModel::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);
-                               if (i == 0) { npro->updateC(read.getReadSeq()); }
+                               if (!read.isLowQuality()) {
+                                 mld != NULL ? mld->update(read.getReadLength(), 1.0) : gld->update(read.getReadLength(), 1.0);
+                                 if (i == 0) { npro->updateC(read.getReadSeq()); }
+                               }
+                               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); }
@@ -315,17 +318,18 @@ void SingleModel::collect(const SingleModel& o) {
        npro->collect(*(o.npro));
 }
 
+//Only master node can call
 void SingleModel::read(const char* inpF) {
        int val;
        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);
@@ -334,14 +338,18 @@ void SingleModel::read(const char* inpF) {
        pro->read(fi);
        npro->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 be called at EM.cpp
 void SingleModel::write(const char* outF) {
        FILE *fo = fopen(outF, "w");
 
@@ -418,9 +426,8 @@ bool SingleModel::simulate(int rid, SingleRead& read, int& sid) {
                }
        }
 
-       std::ostringstream stdout;
-       stdout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos;
-       name = stdout.str();
+       strout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos;
+       name = strout.str();
 
        read = SingleRead(name, readseq);
 
@@ -437,7 +444,7 @@ void SingleModel::finishSimulation() {
 
 void SingleModel::calcMW() {
   double probF, probR;
-  
+
   assert(seedLen >= OLEN && (mld == NULL ? gld->getMinL() : mld->getMinL()) >= seedLen);
   
   memset(mw, 0, sizeof(double) * (M + 1));