For genome BAM, modified MD tag accordingly

[rsem.git] / RSPD.h

diff --git a/RSPD.h b/RSPD.h
index dd397830f455ecd7b3321bc09ff2d559b5fee941..8c484a5d95bbe1ed81d6d2f5adce1a1ea60c58a4 100644 (file)
--- a/RSPD.h
+++ b/RSPD.h
@@ -1,6 +1,10 @@
 #ifndef RSPD_H_
 #define RSPD_H_
 
+#include<cstdio>
+#include<cstring>
+#include<cassert>
+
 #include "utils.h"
 #include "RefSeq.h"
 #include "Refs.h"
@@ -18,7 +22,7 @@ public:
                cdf = new double[B + 2];
 
                //set initial parameters
-               memset(pdf, 0, sizeof(double) * (B + 2));
+               memset(pdf, 0, sizeof(double) * (B + 2)); // use B + 2 for evalCDF
                memset(cdf, 0, sizeof(double) * (B + 2));
                for (int i = 1; i <= B; i++) {
                        pdf[i] = 1.0 / B;
@@ -137,17 +141,17 @@ void RSPD::read(FILE *fi) {
        delete[] cdf;
 
        int val;
-       fscanf(fi, "%d", &val);
+       assert(fscanf(fi, "%d", &val) == 1);
        estRSPD = (val != 0);
 
        if (estRSPD) {
-               fscanf(fi, "%d", &B);
+               assert(fscanf(fi, "%d", &B) == 1);
                pdf = new double[B + 2];
                cdf = new double[B + 2];
                memset(pdf, 0, sizeof(double) * (B + 2));
                memset(cdf, 0, sizeof(double) * (B + 2));
                for (int i = 1; i <= B; i++) {
-                       fscanf(fi, "%lf", &pdf[i]);
+                       assert(fscanf(fi, "%lf", &pdf[i]) == 1);
                        cdf[i] = cdf[i - 1] + pdf[i];
                }
        }