BEGIN{FS=OFS="\t";
#http://bowtie-bio.sourceforge.net/manual.shtml#default-bowtie-output
    q="IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII";
}{
    if (substr($1,1,1)!="@"){
	fl=$2;refid=$3;refst=$4;eddist=0;
	readseq=$10;
	st="+";
	if (fl>0){st="-"};
	l=length(readseq);
	for (i=12;i<=NF;i++){
	    if (substr($i,1,2)=="NM"){
		n=split($i,a,":");eddist=a[n];
	    }
	    if (substr($i,1,2)=="MD"){
		n=split($i,a,":");ed=a[n];
	    }
	}
#    for (i=1;i<=eddist;i++){
	ed2="";ntc=0;
	if (eddist>0){
#	print "MM:"eddist,ed
	    pos=0;x=0;p=length(ed);ntc=0;nntc=0;
	    for (i=1;i<=p;i++){
		c=substr(ed,i,1);
		if (0+c==c){r=1;
		    x=x*10+c;#print i" "c" "x"n";
		}else{
		    if(r==1) {pos+=x+1;}#x matches and current char
			mutb=substr(readseq,pos,1);
			bpos=pos-1;if(st=="-"){bpos=l-pos;}
			ntc++;tcp[ntc]=bpos;tcp1[ntc]=toupper(c);tcp2[ntc]=toupper(mutb);
#			print c"to"mutb" pos"bpos;
#		    if ((c=="T")&&(mutb=="C")){ntc++;tcp[ntc]=refst+pos-1;
#		    print c"to"mutb" pos"pos;
#		}else{
#		    nntc++;
#		}
		    r=0;x=0;
		}
	    }
	    ntntc+=nntc;
	    if (ntc>0){
		nttc+=ntc;
#		print $0;
#	    printf("%s", refid)
#	    for (i=1;i<=ntc;i++){}
	    }
	}
	printf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t", $1,st,$3,$4-1,readseq,substr(q,1,l),0)
	for (i=1;i<=ntc;i++){
	    if (st=="+"){printf("%d:%s>%s",tcp[i],tcp1[i],tcp2[i]);}
	    if (st=="-"){printf("%d:%s>%s",tcp[ntc-i+1],tcp1[ntc-i+1],tcp2[ntc-i+1]);}
	    if (i<ntc){printf(",");}
	}
	printf("\n");
    }
}