#!/usr/bin/perl
use strict;
use warnings;
use constant { RIGHT=>1, LEFT=>0, NAME=>2 };

my(@repeats,@genes, @t47);

loadFile(\@genes,"genes-g38-201505-nodoppel-chr1.csv",0,1,3);
loadFile(\@repeats,"repeats-g38-201505-nodoppel-chr1.csv",1,2,3);
loadFile(\@t47,"47k-80-80-ignore-random-noreverse-chr1.csv",0,1,2);

my $tl=@t47;
my $gl=@genes;
my $rl=@repeats;
my ($gi, $ri)=(0,0);
$|=1;
for(my $ti=0;$ti<$tl;$ti++) {
  $gi++ while($genes[$gi][RIGHT] <= $t47[$ti][LEFT] && $gi<$gl);
  $ri-- while($repeats[$ri][RIGHT] > $t47[$ti][RIGHT] && $ri>0);
  $ri++ while($repeats[$ri][RIGHT] <= $t47[$ti][RIGHT] && $ri<$rl);
  next if($t47[$ti][LEFT] <= $genes[$gi][LEFT] ||
          $t47[$ti][RIGHT] <= $repeats[$ri][LEFT] ||
          $t47[$ti][LEFT] >= $genes[$gi][RIGHT] ||
          $t47[$ti][RIGHT] >= $repeats[$ri][RIGHT]
          );
  print join(',',@{$t47[$ti]},$genes[$gi][NAME],$repeats[$ri][NAME]),"\n";
}

sub loadFile {
  my $o=shift;
  my $name=shift;
  open(my $fl,"<",$name) or die("Can't open file $name\n");
  while(<$fl>) {
   chomp;
   my @r=(split(/,/))[@_];
   push @{$o}, \@r;
  }
}