Improved warning messages in rsem-gen-transcript-plots

[rsem.git] / SamParser.h

diff --git a/SamParser.h b/SamParser.h
index c5a503554b8c9cf4716b722d47da5f8c5db8540c..9d62eff0402ba2eca240b686b598ea3b36324ea4 100644 (file)
--- a/SamParser.h
+++ b/SamParser.h
@@ -112,8 +112,7 @@ int SamParser::parseNext(SingleRead& read, SingleHit& hit) {
        bool canR = (samread(sam_in, b) >= 0);
        if (!canR) return -1;
 
-       if (b->core.flag & 0x0001) { fprintf(stderr, "Find a paired end read in the file!\n"); exit(-1); }
-       //(b->core.flag & 0x0100) &&  && !(b->core.flag & 0x0004)
+       general_assert(!(b->core.flag & 0x0001), "Find a paired end read in the file!");
 
        int readType = getReadType(b);
        std::string name = getName(b);
@@ -143,8 +142,7 @@ int SamParser::parseNext(SingleReadQ& read, SingleHit& hit) {
        bool canR = (samread(sam_in, b) >= 0);
        if (!canR) return -1;
 
-       if (b->core.flag & 0x0001) { fprintf(stderr, "Find a paired end read in the file!\n"); exit(-1); }
-       //assert(!(b->core.flag & 0x0001)); //(b->core.flag & 0x0100) &&  && !(b->core.flag & 0x0004)
+       general_assert(!(b->core.flag & 0x0001), "Find a paired end read in the file!");
 
        int readType = getReadType(b);
        std::string name = getName(b);
@@ -175,11 +173,8 @@ int SamParser::parseNext(PairedEndRead& read, PairedEndHit& hit) {
        bool canR = ((samread(sam_in, b) >= 0) && (samread(sam_in, b2) >= 0));
        if (!canR) return -1;
 
-       if (!((b->core.flag & 0x0001) && (b2->core.flag & 0x0001))) {
-               fprintf(stderr, "One of the mate is not paired-end! (RSEM assumes the two mates of a paired-end read should be adjacent)\n");
-               exit(-1);
-       }
-       //assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001));
+       general_assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001), \
+                       "One of the mate is not paired-end! (RSEM assumes the two mates of a paired-end read should be adjacent)");
 
        bam1_t *mp1 = NULL, *mp2 = NULL;
 
@@ -226,11 +221,8 @@ int SamParser::parseNext(PairedEndReadQ& read, PairedEndHit& hit) {
        bool canR = ((samread(sam_in, b) >= 0) && (samread(sam_in, b2) >= 0));
        if (!canR) return -1;
 
-       if (!((b->core.flag & 0x0001) && (b2->core.flag & 0x0001))) {
-               fprintf(stderr, "One of the mate is not paired-end! (RSEM assumes the two mates of a paired-end read should be adjacent)\n");
-               exit(-1);
-       }
-       //assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001));
+       general_assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001), \
+                       "One of the mate is not paired-end! (RSEM assumes the two mates of a paired-end read should be adjacent)");
 
        bam1_t *mp1 = NULL, *mp2 = NULL;