Notes on the map program:

1) To compile map.c, use a command like this:
       cc -o map map.c -lm

2) Documentation:

NOTE: Please make sure you have the right number of loci.
The number of loci should be the total number of loci in
the current order(s), including the 'trait' locus.  There
is no checking if you've entered this number correctly.

  This will convert LINKMAP output into a multipoint
  lod score curve, provided that the trait marker has
  been started off the map on the left (with a theta
  of 0.50).

This program is designed to convert LINKMAP output 
into columnar data with standardized
lod scores. The data file should be set up as follows:
   LOCUS ORDER :  1 2 3 4
THETAS 0.5 0.2 0.1  
TOTALS 112.0 12.0 

Under SUN unix, you can create such a file by using the command:
 egrep 'Order|TH|TO' final.out > map.out  
Such a set-up is the standard output from the SEARCH command under VMS.
Note that it is important to have a blank starting the line on the orders
and a T starting the line with the thetas and totals.
Also, the trait locus MUST be started on the left in order to provide correct
standardization.

A sample input file:

	Locus Order                : 1 8 11
THETAS  0.500 0.079
TOTALS     -473.503571  -205.639550
THETAS  0.400 0.079
TOTALS     -470.635961  -204.394165
THETAS  0.300 0.079
TOTALS     -468.168263  -203.322460
THETAS  0.200 0.079
TOTALS     -466.617404  -202.648932
THETAS  0.100 0.079
TOTALS     -466.717990  -202.692616
THETAS  0.000 0.079
TOTALS     -495.168376  -215.048435
	Locus Order                : 8 1 11
THETAS  0.000 0.079
TOTALS     -495.168376  -215.048435
THETAS  0.016 0.065
TOTALS     -479.464454  -208.228323
THETAS  0.032 0.051
TOTALS     -478.697663  -207.895311
THETAS  0.047 0.035
TOTALS     -479.305106  -208.159119
THETAS  0.063 0.018
TOTALS     -481.468460  -209.098650


Output:

The map.out file will be in Cricket Graph format, ready for
drawing.  However, maps of the same area using different
sets of loci must be aligned manually by shifting their origins.

The summary file contains columns of information, which
represent the following information:

   Loci    Distance   Thetas       LOD         likelihoods

  1  8 11  -99.000 0.500 0.079   0.00000  -205.63955  -205.63955
  1  8 11   -0.805 0.400 0.079   1.24539  -204.39416  -205.63955
  1  8 11   -0.458 0.300 0.079   2.31709  -203.32246  -205.63955
  1  8 11   -0.255 0.200 0.079   2.99062  -202.64893  -205.63955
  1  8 11   -0.112 0.100 0.079   2.94693  -202.69262  -205.63955
  1  8 11    0.000 0.000 0.079  -9.40888  -215.04844  -205.63955
  8  1 11    0.000 0.000 0.079  -9.40888  -215.04844  -205.63955
  8  1 11    0.016 0.016 0.065  -2.58877  -208.22832  -205.63955
  8  1 11    0.033 0.032 0.051  -2.25576  -207.89531  -205.63955
  8  1 11    0.049 0.047 0.035  -2.51957  -208.15912  -205.63955

I apologize for the scanty documentation.  If you encounter
any bugs or have any questions, please do not hesitate
to contact me.

********************************
| Daniel E. Weeks, Ph.D.       | 
| Department of Human Genetics |  Internet: 
| University of Pittsburgh     |    dweeks@watson.hgen.pitt.edu
| Crabtree Hall, Room A310     |
| 130 DeSoto Street            |  
| Pittsburgh, PA 15261         | 
|                              |
| (412) 624-3066               |
| FAX: (412) 624-3020          |
********************************