Support for X and = in CIGAR strings

Author: karel-brinda

wgsim_eval.pl

@@ -48,7 +48,7 @@ sub alneval {
 		my ($q, $is_correct, $chr, $left, $rght) = (int($t[4]/10), 1, $t[2], $t[3], $t[3]);
 		$max_q = $q if ($q > $max_q);
 		# right coordinate
-		$_ = $t[5]; s/(\d+)[MDN]/$rght+=$1,'x'/eg;
+		$_ = $t[5]; s/(\d+)[MDN=X]/$rght+=$1,'x'/eg;
 		--$rght;
 		# correct for clipping
 		my ($left0, $rght0) = ($left, $rght);
@@ -287,7 +287,7 @@ sub uniqcmp_aux {
 	my ($x, $nm) = (0, 0);
 	$nm = $1 if (/NM:i:(\d+)/);
 	$_ = $t[5];
-	s/(\d+)[MI]/$x+=$1/eg;
+	s/(\d+)[M=XI]/$x+=$1/eg;
 	@{$a->{$t[0]}[$which]} = (($t[1]&0x10)? 1 : 0, $t[2], $t[3]-$l, $t[4], "$x:$nm", $x - $b * $nm);
   }
   close($fh);