This document contains information for the simulation program for
"Distributions of positive signals in pyrosequencing".

The name of the simulation program is "sbs_ffcm_r.c".  The structure and
usage of the program is very similar to "sbs_ffcm_simul.c", the program
to simulate sequence length distribution.  Actually "sbs_ffcm_r.c" includes
the functions of "sbs_ffcm_simul.c", and more.  So please also refer to
the "readme.txt" for more information.
 
To compile the program, use something like this:

gcc -o sbs_ffcm_r -W -Wall -O3 sbs_ffcm_r.c -lm

Two binary executables are also included: sbs_ffcm_r_32 for 32-bit computers
and sbs_ffcm_r_64 for 64-bit computers.

To run the program, 

./sbs_ffcm_r -f 10 -r 2000000 -a 0.333333333 -b 0.090909091 -c 0.432900433 -d 0.142857143 -A 1 -B 1 -C 1 -D 1


The file "sbs_ffcm_r_100_repeat_20000000_A0.333_1.00_B0.091_1.00_C0.433_1.00_D0.143_1.00" contains the output of
a sample simulation run.

Yong Kong
Yale University