my @a;

while(<INA>){
  chomp;
  /^([^\t]*)\t([^\t]*)\t([^\t]*)\t([^\t]*)\t([^\t]*)\t/;
  if($2 eq $c){
    push(@a,[$3,($3 eq '+')?($4):($5)]);
  }
}

close INA;



foreach (@a){

  my $la = $_->[1]+$optTSS;
  my $lb = $_->[1]-$optTSS;

  print "$la,$lb\n";                  # it prints $la,$lb here
  for(my $i =$la; $i <=$lb;$i++){ # loop is skipped no printing
    print "$la,$lb,$i";
  };

  print ">\n";
}