Deleted a ';' at the end of RSEM v1.2.15 updates

[rsem.git] / SamParser.h

diff --git a/SamParser.h b/SamParser.h
index 513536f2a2107e181a0393946a00e9fa77c35416..81d4097cf0033dee55d012abeaf8ea106120b9d9 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();
 
        /**
@@ -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();
@@ -341,10 +341,17 @@ inline int SamParser::getReadType(const bam1_t* b) {
        return (bam_aux2i(p) > 0 ? 2 : 0);
 }
 
-
 //For paired-end reads, do not print out type 2 reads
 inline int SamParser::getReadType(const bam1_t* b, const bam1_t* b2) {
-       if ((b->core.flag & 0x0002) && (b2->core.flag & 0x0002)) return 1;
+       if (!(b->core.flag & 0x0004) && !(b2->core.flag & 0x0004)) return 1;
+
+       if (!strcmp(rtTag, "")) return 0;
+
+       uint8_t *p = bam_aux_get(b, rtTag);
+       if (p != NULL && bam_aux2i(p) > 0) return 2;
+
+       p = bam_aux_get(b2, rtTag);
+       if (p != NULL && bam_aux2i(p) > 0) return 2;
 
        return 0;
 }