RGA_eland - Reference Guided Assember using ELAND results. It does:
  1. calcuate the real coverage of Solexa microreads to the reference sequence(s)
  2. report the coordinates of all the maximum contigs and length
  3. output density graphes of chromosome size (optional)

  Note: only takes microreads with the unique hits [U0, U1, U2] from ELAND results

Usage: perl RGA_eland_rc1.pl options
 required:
  -r    Reference size file [only the SIZE of each chromosome, e.g.,
                chr1[TAB]29231457
                [NOTE: [TAB] means tab-delimited; chromosome names should be the same as that in ELAND file]
  -l    ELAND result file
 optional:
  -m    Mismatches: a string of U0,U1,U2 without space, e.g., U0, U0U1, U1U2, U0U1U2 [default: U0]
  -p    Switch of Plotting or not [default: not plot; need gnuplot version 4.2.2 or above]