foreach $match ( @{ $matches } )
{
- if ( $match->{ "DIR" } =~ /^f/ )
+ if ( ($match->{ "DIR" } and $match->{ "DIR" } =~ /^f/) or ($match->{ "STRAND" } and $match->{ "STRAND" } eq '+') )
{
print $fh_forward join( "\t", $match->{ "Q_BEG" } + 1, $match->{ "S_BEG" } + 1 ), "\n";
print $fh_forward join( "\t", $match->{ "Q_END" } + 1, $match->{ "S_END" } + 1 ), "\n";