use strict;
use warnings;
use Data::Dumper;

#declarations
my @rawfile;
my $filter_count=0;

#input
open(INFILE, "<$ARGV[0]") || die "cannot open file:$!";

####
#filter file
#------------------
#  parse entire file
my $header = <INFILE>;    #grabbing header
chomp $header;
my @headerArray = split("\t", $header);
my $sizeheader=@headerArray;

for my $line (<INFILE>) {
    chomp $line;
    my @splitline = split("\t", $line);
    #my $poskey = $splitline[0] . ":" . $splitline[1];

    for (@splitline){
	if (/^$ARGV[1]/){
	    $filter_count++;
	    push(@rawfile,$line);
	}
    }
  
}
close INFILE;
print "Completed filtering $ARGV[0]\n";
print "Found $filter_count elements\n";
my $outfilename = substr($ARGV[0],0,length($ARGV[0])-4)."_filter.txt";
print "Filtering to output file: $outfilename\n";

####
#output file
#------------------
open(OUTFILE, ">$outfilename") || die "cannot open file to write: $!";
print OUTFILE "$header\n";

for (@rawfile) {
    print OUTFILE "$_\n";
}
close OUTFILE;