X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=SamParser.h;h=81d4097cf0033dee55d012abeaf8ea106120b9d9;hp=513536f2a2107e181a0393946a00e9fa77c35416;hb=92b24279a3ecc72946e7e7c23149ad0d181f373a;hpb=fb2aa1ca9d00710943155ef3abbbdd87df116e4a

diff --git a/SamParser.h b/SamParser.h
index 513536f..81d4097 100644
--- 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;
 }