#!/usr/bin/perl -w
use strict;
use Data::Dumper;




# sub routinen
###########################


sub read_gff_file {

    print "Enter the filename of your input file with the single columns of your gff file:= ";          

    chomp( my $gfffilename=<STDIN> );

    open my $gff_fh, '<', $gfffilename or die "$gfffilename Can not open file\n";
    # nur erste Zeile lesen
    chomp( my $gff = <$gff_fh> );

    return split m{ }, $gff;
}

sub open_var_file {

    print "Enter the filename of your input file with the variants:= ";         

    chomp( my $varfilename=<STDIN> );

    open my $var_fh, '<',$varfilename or die "$varfilename Can not open file\n";
    # keine Zeile lesen, nur Handle liefern
    return $var_fh;
}

sub do_my_job {

    my @spalten = read_gff_file();
    my $var_handle = open_var_file();

    while ( my $line = <$var_handle> ) {
        
        chomp $line;

        # Sollte 3 Felder (z.B. A,A1,A2) ergeben
        my @fields = split m{ }, $line;

        my @result = @spalten;
        splice(@result, 2, 0, @fields );

        print join( ', ', @result ), "\n";
    }
}


# main program
###########################

do_my_job();