convert XA to multiple lines

xa2multi.pl

@@ -0,0 +1,16 @@
+#!/usr/bin/perl -w
+
+use strict;
+use warnings;
+
+while (<>) {
+	if (/\tXA:Z:(\S+)/) {
+		my $l = $1;
+		print;
+		my @t = split("\t");
+		while ($l =~ /([^,;]+),([-+]\d+),([^,]+),(\d+);/g) {
+			my $mchr = ($t[6] eq $1)? '=' : $t[6]; # FIXME: TLEN/ISIZE is not calculated!
+			print(join("\t", $t[0], 0x100|($t[1]&0x6e9)|($2<0?0x10:0), $1, abs($2), 0, $3, @t[6..7], 0, @t[9..10], "NM:i:$4"), "\n");
+		}
+	} else { print; }
+}