--bowtie-chunkmbs

[rsem.git] / SingleModel.h

diff --git a/SingleModel.h b/SingleModel.h
index 756e3d5cdecf386339eb90c303e9aa6b908a26e5..97ffd29c8ce9b7d499d99979bf0d51546cb17ab7 100644 (file)
--- a/SingleModel.h
+++ b/SingleModel.h
@@ -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); }
@@ -321,12 +324,12 @@ void SingleModel::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);
@@ -339,7 +342,7 @@ void SingleModel::read(const char* inpF) {
                if (M == 0) M = val;
                if (M == val) {
                        mw = new double[M + 1];
-                       for (int i = 0; i <= M; i++) fscanf(fi, "%lf", &mw[i]);
+                       for (int i = 0; i <= M; i++) assert(fscanf(fi, "%lf", &mw[i]) == 1);
                }
        }
 
@@ -441,7 +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));