while () {
    chomp $_;
    my @v = split( /t/, $_ );
    get_pid(@v);
}
 
sub get_pid {
    my @line = @_;
    my $pid = ( 100.0 - ( &pslCalcMilliBad(@line) * 0.1 ) );
    print "The percentage: $pidn";
 
    #return $pid;
}
 
sub pslCalcMilliBad {
    my @cols = @_;
 
    # sizeNul depens of dna/Prot
    my $sizeMul = 1;
 
    #if ($option{p}) {
    #        $sizeMul = 3;
    #} else {
    #        $sizeMul = 1;
    #}
 
    # cols[0]  matches
    # cols[1]  misMatches
    # cols[2]  repMaches
    # cols[4]  qNumInsert
    # cols[6]  tNumInsert
    # cols[11] qStart
    # cols[12] qEnd
    # cols[15] tStart
    # cols[16] tEnd
 
    my $qAliSize = $sizeMul * ( $cols[12] - $cols[11] );
    my $tAliSize = $cols[16] - $cols[15];
 
    # I want the minimum of qAliSize and tAliSize
    my $aliSize;
    $qAliSize < $tAliSize ? $aliSize = $qAliSize : $aliSize = $tAliSize;
 
    # return 0 is AliSize == 0
    return 0 if ( $aliSize <= 0 );
 
    # size diff
    my $sizeDiff = $qAliSize - $tAliSize;
    if ( $sizeDiff < 0 ) {
        $sizeDiff = 0;
 
        #if ($option{m}) {
        #$sizeDiff = 0;
        #} else {
        #$sizeDiff = -($sizeDiff);
        #}
    }
 
    # insert Factor
    my $insertFactor = $cols[4];
 
    #$insertFactor += $cols[6] unless ($option{m});
    my $milliBad = (
        1000 * (
            $cols[1] * $sizeMul +
              $insertFactor +
              &round( 3 * log( 1 + $sizeDiff ) )
        )
    ) / ( $sizeMul * ( $cols[0] + $cols[2] + $cols[1] ) );
    return $milliBad;
 
}
 
sub round {
    my $number = shift;
    return int( $number + .5 );
}