$input_file = "/ddn/gs1/home/bennettb/references/chromhmm/hg38/chromhmm_harriet6.bed";
$output_file = "chromHMM_Harriet6.bed";
$output_file_bigbed = "chromHMM_Harriet6.bigBed";
$chrom_sizes_file = "/ddn/gs1/home/bennettb/references/ucsc/hg38.noAlt.chromSizes";
%colors = (
  TSS => '255,0,0',
  Promoter => '112,48,160',
  Transcription => '0,128,0',
  Enhancers => '255,195,77',
  Repressed => '138,145,208',
  Other => '128,128,128'
);

open( IN, "<".$input_file );
open( OUT, ">".$output_file );

$i = 1;
while( $L = <IN> ) {
    chomp( $L );
    @D = split( /\t/, $L );
    print OUT $L."\t1000\t+\t".$D[1]."\t".$D[2]."\t".$colors{$D[3]}."\n";
    $i++;
}

close( IN );
close( OUT );

system( "sort -k1,1 -k2,2n ".$output_file." > ".$output_file.".sorted" );
system( "/ddn/gs1/home/bennettb/tools/ucsc_18.07.24/bedToBigBed ".$output_file.".sorted ".$chrom_sizes_file." ".$output_file_bigbed );
system( "rm -f ".$output_file );
system( "rm -f ".$output_file.".sorted" );