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lib/App/Egaz/Command/lav2psl.pm  view on Meta::CPAN

            my ( @sizes, @q_begins, @t_begins );

            my @align_pieces = $a_stanza =~ /\s*l (\d+ \d+ \d+ \d+ \d+)/g;
            my $t_former_end;
            my $q_former_end;
            for my $align_piece (@align_pieces) {

                unless ( $align_piece =~ /(\d+) (\d+) (\d+) (\d+) (\d+)/g ) {
                    Carp::croak "l-line error\n";
                }
                my ( $t_begin, $q_begin, $t_end, $q_end, $percent_id ) = ( $1, $2, $3, $4, $5 );
                $t_begin--;
                $q_begin--;
                $percent_id = 0.01 * $percent_id;

                my $bases       = $q_end - $q_begin;
                my $match_piece = App::Egaz::Common::round( $percent_id * $bases );
                $match += $match_piece;
                $mismatch += $bases - $match_piece;

                if ( $t_former_end and $t_begin != $t_former_end ) {
                    $t_num_ins++;
                    $t_base_ins += $t_begin - $t_former_end;
                }
                if ( $q_former_end and $q_begin != $q_former_end ) {
                    $q_num_ins++;
                    $q_base_ins += $q_begin - $q_former_end;