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

[rsem.git] / SamParser.h

diff --git a/SamParser.h b/SamParser.h
index e91f9c379539fc7ada0f8682bcfc7c957489d67f..4747ef4281af593f714450d68ccfc65090662891 100644 (file)
--- a/SamParser.h
+++ b/SamParser.h
@@ -25,7 +25,7 @@
 
 class SamParser {
 public:
-       SamParser(char, const char*, Transcripts&, const char* = 0);
+       SamParser(char, const char*, const char*, Transcripts&, const char*);
        ~SamParser();
 
        /**
@@ -62,7 +62,7 @@ private:
        }
 
        std::string getName(const bam1_t* b) {
-               return std::string((char*)bam1_qname(b));
+               return std::string(bam1_qname(b));
        }
 
        std::string getReadSeq(const bam1_t*);
@@ -80,7 +80,7 @@ private:
 char SamParser::rtTag[STRLEN] = ""; // default : no tag, thus no Type 2 reads
 
 // aux, if not 0, points to the file name of fn_list
-SamParser::SamParser(char inpType, const char* inpF, Transcripts& transcripts, const char* aux)
+SamParser::SamParser(char inpType, const char* inpF, const char* aux, Transcripts& transcripts, const char* imdName)
        : transcripts(transcripts)
 {
        switch(inpType) {
@@ -93,7 +93,7 @@ SamParser::SamParser(char inpType, const char* inpF, Transcripts& transcripts, c
        header = sam_in->header;
        general_assert(header != 0, "Fail to parse sam header!");
 
-       transcripts.buildMappings(header->n_targets, header->target_name);
+       transcripts.buildMappings(header->n_targets, header->target_name, imdName);
 
        b = bam_init1();
        b2 = bam_init1();
@@ -190,6 +190,8 @@ int SamParser::parseNext(PairedEndRead& read, PairedEndHit& hit) {
                mp1 = b2; mp2 = b;
        }
 
+       general_assert(!strcmp(bam1_qname(mp1), bam1_qname(mp2)), "Detected a read pair whose two mates have different names: " + getName(mp1) + " , " + getName(mp2) + " !");
+
        int readType = getReadType(mp1, mp2);
        std::string name = getName(mp1);
 
@@ -242,6 +244,8 @@ int SamParser::parseNext(PairedEndReadQ& read, PairedEndHit& hit) {
                mp1 = b2; mp2 = b;
        }
 
+       general_assert(!strcmp(bam1_qname(mp1), bam1_qname(mp2)), "Detected a read pair whose two mates have different names: " + getName(mp1) + " , " + getName(mp2) + " !");
+
        int readType = getReadType(mp1, mp2);
        std::string name = getName(mp1);