/* intervalToBed - Simple little paraFlow utility ... yeah a fancy awk */
/* could've done the job too. */

to usage() 
   {
   prin('
Convert simple WindowMasker output into BED 5.  The 5th column is all 1000,
which is dumb, but the score will be used in similar BED 5 tables from other
denovo repeat programs.
usage:
   intervalToBed input.int output.bed
');
   }

to intervalToBed(string input, string output)
   {
   file intFile = fileOpen(args[0], 'r');
   file bedFile = fileOpen(args[1], 'w');
   string chrom = intFile.readLine().trim().rest(5);
   int repNum = 1;
   for (line in intFile.readLine())
       {
       array of string parts = line.split(" -\n");
       int start = parts[0].asInt();
       int end = parts[3].asInt() + 1;
       bedFile.write("$chrom\t$start\t$end\t$chrom.$repNum\t1000\n");
       repNum += 1;
       }
   }

/*** Main! ***/

if (args.size == 2)
   intervalToBed(args[0], args[1]);
else
   usage();