Added error detection for cases such as a read's two mates having different names...

[rsem.git] / parseIt.cpp

diff --git a/parseIt.cpp b/parseIt.cpp
index 3373ef280979428230b74d77439d61bff3a96d47..f40f82295302c48b16923d6655f3757d4057e09b 100644 (file)
--- a/parseIt.cpp
+++ b/parseIt.cpp
@@ -52,7 +52,7 @@ void init(const char* imdName, char alignFType, const char* alignF) {
 
        char* aux = 0;
        if (strcmp(fn_list, "")) aux = fn_list;
-       parser = new SamParser(alignFType, alignF, transcripts, aux);
+       parser = new SamParser(alignFType, alignF, aux, transcripts, imdName);
 
        memset(cat, 0, sizeof(cat));
        memset(readOutFs, 0, sizeof(readOutFs));
@@ -94,6 +94,9 @@ void parseIt(SamParser *parser) {
                                record_read.write(n_os, cat[record_val]);
                                ++N[record_val];
                        }
+
+                       general_assert(record_val == 1 || hits.getNHits() == 0, "Read " + record_read.getName() + " is both unalignable and alignable according to the input SAM/BAM file!");
+
                        // flush out previous read's hits if the read is alignable reads
                        if (record_val == 1) {
                                hits.updateRI();