--- tophat-2.0.10/src/bam2fastx.cpp	2013-06-20 03:36:08.000000000 +0100
+++ bam2fastx.cpp	2014-02-02 18:20:31.000000000 +0000
@@ -192,11 +192,11 @@
 	if (!is_fastq) return;
 	if (color) {
       qual = (unsigned char*)bam1_qual(b);
-	  rd.qual.resize(seqlen-1);
-	  for(i=1;i<seqlen;i++) {
+	  rd.qual.resize(seqlen);
+	  for(i=0;i<seqlen;i++) {
 	    if (qual[i]==0xFF)
 	      rd.qual[i]='I';
-	    else rd.qual[i-1]=qual[i]+33;
+	    else rd.qual[i]=qual[i]+33;
 	  }
 	}
 	else {