Prerequisite
=====================================
The Genehunter plus executable (namely "ghp" ) should be accessible 
from the STepc working directory. 


Command Line Syntax
=====================================

  stepc [-f parameter_file]

if the "parameter_file option is not specified, STepc looks
for the file "param.dat" in current working directory.


Input Files 
====================================

STepc requires 3 input files: a marker file, a pedigree data file 
and a parameter file. 

The marker file and pedigree data file are in LINKAGE format, 
for detailed information please refer to the web page 
http://linkage.rockefeller.edu/soft/linkage/, section DATAFILE 
and section PEDFILE. 

Parameter file specifies following parameters used by STepc:

1.DATA_FILE(mandatory): the path to find the pedigree data file,
it could either be a absolute path or a relative path to current
working directory. e.g.  
       
DATA_FILE /home/guest/ped_file  
DATA_FILE ped_file (relative path, refer to the file "ped_file" in 
current working path )
          
2.MARKER_FILE(mandatory): the path to find the marker file. it 
could either be a absolute path or a relative path to current 
working directory.

3. START_MARKER_LIST ... END_MARKER_LIST (mandatory): a list of markers
to be tested by STepc. e.g. 

START_MARKER_LIST 
SNP20 SNP66 SNP45 SNP44 SNP43 SNP79 SNP78 SNP77 
END_MARKER_LIST

Note, the name of markers should be consistent with their description 
in MARKER_FILE (e.g.  "3   2  # SNP44" ).The marker is ignored from 
the if corresponding name not presented in MARKER_FILE.

4. GHP_PATH (optional): the path to find Genehunter plus executable 
"ghp". If not specified, STepc searches environment variable PATH for 
ghp executable (usually, in /usr/local/bin , /usr/bin/ etc. ), if 
the attempt fails, STepc quits and outputs error message "GHP_PATH 
not defined".

5. PDF_PLOT [on/off] (optional): the option to plot test results in pdf 
files.

* Comments in parameter file: the comment contents in each line
starts with symbol "#" or "//", STepc ignores followed content until
end of the line.