#! /opt/mambaforge/envs/bioconda/conda-bld/gmap_1685188587992/_build_env/bin/perl


use Getopt::Std;
$opt_s = 0;	     # starting column (UCSC track can start in column 0 or 1)
getopts("s:");


while (defined($line = <>)) {
    $line =~ s/\r\n/\n/;
    chop $line;
    @fields = split /\t/,$line;

    $acc = $fields[$opt_s + 0];
    $chr = $fields[$opt_s + 1];
    #$chr =~ s/chr//;
    #$chr =~ s/_random/U/;

    $strand = $fields[$opt_s + 2];
    @starts = split ",",$fields[$opt_s + 8];
    @ends = split ",",$fields[$opt_s + 9];

    $nexons = $#starts + 1;
    if ($nexons != $fields[$opt_s + 7]) {
	print STDERR "Reported number of exons $fields[$opt_s + 7] != observed $nexons: Skipping $line\n";

    } elsif ($strand eq "+") {
	printf ">$acc $chr:%u..%u\n",$starts[0] + 1,$ends[$#ends];
	print "$acc\n";
	for ($i = 0; $i < $nexons; $i++) {
	    printf "%u %u\n",$starts[$i] + 1,$ends[$i];
	}
    } elsif ($strand eq "-") {
	@starts = reverse @starts;
	@ends = reverse @ends;
	printf ">$acc $chr:%u..%u\n",$ends[0],$starts[$#starts] + 1;
	print "$acc\n";
	for ($i = 0; $i < $nexons; $i++) {
	    printf "%u %u\n",$ends[$i],$starts[$i] + 1;
	}
    } else {
	print STDERR "Strand is neither + nor -: Skipping $line\n";
    }
}

exit;

