RUNNING

The programs "hiv_sim" and "hiv_sim_gui" are built using "make" in the Linux subdirectory.  For building requirements, 
see the file BUILDING.  When running you may need to load the Mesa module and put "lib" directory of
the directory you set in the GTKGLEXT environment variable (see BUILDING) in the front of the path
specified by the LD_LIBRARY_PATH environment variable (see sample export command below).

    export LD_LIBRARY_PATH="$GTKGLEXT/lib:$LD_LIBRARY_PATH"

The program requires an "input" file (hiv_sim.in by default) and takes an optional "criteria" file (hiv_sim.crit by default).
The input file contains input variable names and values placing one per line.  Names may appear multiple times,
but only the last value will be used.  If a variable is not recognized, it is ignored.  Blank lines
and comments are not allowed in this version.  

Input variable details are provided in the file INPUTS.  

The criteria file is used to supply viral and phylogenetic HIV data to match against.
The categories used are detailed in the file CRITERIA.

Finally, the program can be used to generate several different output files.  The most basic 
contains time history date for overall viral load.  Other files can be used to output other 
summary statistics or statistics by spatial region (files are specified using the -w option 
with a bit-wise mask value). There are several advanced options not discussed here as 
illustrated by the usage output below. 


Usage: ./hiv_sim [-h][-l][-f <input_file>][-c <crit file>][-e <entropy file>][-p <pat>][-q <seq file>][-r][-s <seed>][-v][-w <write_mask>]
	-h = this help
	-f = optional input file
	-a = optional follow-on input file (at Input_refresh)
	-c = optional criteria file
	-e = optional entropy file for fitness inheritance (requires -q)
		Format: target mean and variance values for...
			log peak viral load
			time to peak viral load
			log peak-nadir drop in viral load
			time to nadir viral load
			log viral load set point
			log variance from viral load set point
		(set point taken as measure 10 days after nadir)
		(set point variance measured at 10 day intervals)
	-l = viral loads in as log values (for -z)
	-p <patient>= viral loads in as log values (for -z)
	-y = optional sequence sampling schedule file
	-z = optional target viral load file
		currently it must contain N patients each with M time then Vt values for scored fit
		Format:
			<N>
			<M>
			t1
			...
			t<m>
		t1
			...
		t<m>
	-q <seq FASTA>= FASTA file with initial sequence (for a/c/g/t ratios)
	-r = random number seed truely random
	-s <seed> = random number seed for repeating run (unsigned)
	-w <write_mask> = which output (csv) files to generate (Bit-mask)
		1= main compartment counts vs time
		2= strains and their cell counts vs time
		4= strain lineage information (birth, parent, etc.)
		8= top 10 strain ids and viral loads