The repeatSelect program is a little complicated.  The algorithm is as follows:
start with the RepeatMasks, and discard denovo repeats that are masked.  Then
sort the repeats by copy number, mean score, total bases covered, or something
like that.  Then go through the list repeats and output ones until we've 
reached the desired amount of additional masking.

Here is an illustration to help explain how it works.  Consider the 
following figure:
     
              1         2         3         4         5         6
Base 123456789012345678901234567890123456789012345678901234567890
Rmsk XXX   XXXX                XXXX                   XXXXXXXXXXX
  R1 ###    ####          ####
  R2             ### ###
  R3                     #          # # # #
  R4                                         ########### 
  R5                           ###

The first row ("Rmsk"), represents RepeatMasker repeats.  R1-R5 are different
denovo repeats.  Here are sample .out files:

(1) Rmsk

   SW  perc perc perc  query     position in query    matching repeat         position in  repeat
score  div. del. ins.  sequence  begin  end (left)   repeat   class/family   begin  end (left)  ID

 2000   0.0  0.0  0.0  Base       1       3    (0) +  Rmsk  Unknown       1   3    (0)       
 3000   0.0  0.0  0.0  Base       7      10    (0) +  Rmsk  Unknown       1   4    (0)       
 5000   0.0  0.0  0.0  Base      27      30    (0) +  Rmsk  Unknown       1   4    (0)
10000   0.0  0.0  0.0  Base      50      60    (0) +  Rmsk  Unknown       1  11    (0)

(2) Denovo

   SW  perc perc perc  query     position in query    matching repeat         position in  repeat
score  div. del. ins.  sequence  begin  end (left)   repeat   class/family   begin  end (left)  ID

 1000   0.0  0.0  0.0  Base       1       3    (0) +  R1 Unknown  1  3    (0)       
 1000   0.0  0.0  0.0  Base       8      11    (0) +  R1 Unknown  1  4    (0)
 5000   0.0  0.0  0.0  Base      13      15    (0) +  R2 Unknown  1  3    (0)
 5000   0.0  0.0  0.0  Base      17      19    (0) +  R2 Unknown  1  3    (0)
 1000   0.0  0.0  0.0  Base      21      21    (0) +  R3 Unknown  1  1    (0)
 1000   0.0  0.0  0.0  Base      22      25    (0) +  R1 Unknown  1  4    (0)
 1000   0.0  0.0  0.0  Base      27      29    (0) +  R5 Unknown  1  3    (0)
 1000   0.0  0.0  0.0  Base      32      32    (0) +  R3 Unknown  1  1    (0)
 1000   0.0  0.0  0.0  Base      34      34    (0) +  R3 Unknown  1  1    (0)
 1000   0.0  0.0  0.0  Base      36      36    (0) +  R3 Unknown  1  1    (0)
 1000   0.0  0.0  0.0  Base      38      38    (0) +  R3 Unknown  1  1    (0)
 1000   0.0  0.0  0.0  Base      41      51    (0) +  R4 Unknown  1 11    (0)

Here's a table of stats:

            Total Coverage     Coverage after masking
Rmsk       22/60 = 37.00 %                        n/a
  R1       11/60 = 18.00 %             4/60 =  6.67 %
  R2        6/60 = 10.00 %             6/60 = 10.00 %
  R3        5/60 =  8.33 %             5/60 =  8.33 %
  R4       11/60 = 18.33 %             9/60 = 15.00 %
  R5        3/60 =  5.00 %             0/60 =  0.00 %

Note that different repeats have different characteristics.

* Needs finishing.
