edit read.h to fix read ID, moved the bam tags to the end of the read

s4hts · Sep 7, 2024 · 156208a · 156208a
1 parent 0f46b5f
commit 156208a
Showing 1 changed file with 6 additions and 3 deletions.
diff --git a/common/src/read.h b/common/src/read.h
@@ -60,9 +60,12 @@ class Read {
     const std::string get_id_fastq(const char& read='\0') const {
         std::string sam_comment = "";
         for (auto const& s : comments) { sam_comment += '|' + s; }
-        std::string tmp = id + ' ' + read;
-        if (!(id2 == "")) tmp = tmp + id2;
-        tmp = tmp + sam_comment;
+        std::string tmp = id;
+        if (!(id2 == "")){
+		 tmp = tmp + ' ' + read + id2 + sam_comment;
+	} else if (!(sam_comment == "")){
+		tmp = tmp + ' ' + read + sam_comment;
+	}
         return tmp;
     }
     const std::string get_id_tab(const char& read='\0') const {