sub get_mismatches { my ($segment, $comp_segment) = @_; my @seg_mismatches; my @seg_mis; my $i; my %good_pairs = ( 'A' => 'T', 'C' => 'G', 'G' => 'C', 'T' => 'A', ); foreach (my $i =0; $i < @$segment; $i++) { if ($segment->[$i] ne $good_pairs {$comp_segment->[$i]}) { push @seg_mismatches,"$segment->[$i-1]$segment->[$i]/$comp_segment->[$i-1]$comp_segment->[$i]\n"; push @seg_mismatches, "$segment->[$i]$segment->[$i+1]/$comp_segment->[$i]$comp_segment->[$i+1]\n"; push @seg_mis, "$segment->[$i-1]$segment->[$i] $segment->[$i]$segment->[$i+1]\n"; } } return (\@seg_mismatches, \@seg_mis); }