From 3536e2113ceef0c4cd5e7b11e89f76dc7043190c Mon Sep 17 00:00:00 2001
From: Tobias Marschall <T.Marschall@cwi.nl>
Date: Wed, 7 Sep 2011 14:31:28 +0200
Subject: [PATCH] Bugfix: reverse (complement) sequence and phred string if
 alternative alignment has different orientation than primary alignment

---
 xa2multi.pl | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/xa2multi.pl b/xa2multi.pl
index 6dae38b..2409c29 100755
--- a/xa2multi.pl
+++ b/xa2multi.pl
@@ -10,7 +10,16 @@ while (<>) {
 		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");
+			my $seq = $t[9];
+			my $phred = $t[10];
+			# if alternative alignment has other orientation than primary, 
+			# then print the reverse (complement) of sequence and phred string
+			if ((($t[1]&0x10)>0) xor ($2<0)) {
+				$seq = reverse $seq;
+				$seq =~ tr/ACGTacgt/TGCAtgca/;
+				$phred = reverse $phred;
+			}
+			print(join("\t", $t[0], 0x100|($t[1]&0x6e9)|($2<0?0x10:0), $1, abs($2), 0, $3, @t[6..7], 0, $seq, $phred, "NM:i:$4"), "\n");
 		}
 	} else { print; }
 }