CMT can be run via the command line as:
	CMT --parameters--

The following arguments can be used to specify each parameter:

-e :	experiment bed file	
-c : 	control bed file
-r :	result text file containing detected regions
-l :	minimum size of the regions (integer, default=200)
-h :	maximum size of the regions (integer, default=10000)
-f :	fragment size (integer, default=200)
-t :	minimum height of detected regions (integer, default=5)
-k :	k-fold value (real) (default=2.0)
-x :	storing experiment and control histograms (boolean - true: store the histograms , false: do not store them) (default=false)

The first three parameters (experiment file, control file and result file) are mandatory, but the rest of parameters 
are optional and in case of not using them, the default value will be used.

An example of calling CMT is as follows:

	CMT -e Exp.bed -c Control.bed -r result.txt -l 200 -h 5000 -k 1.4 -f 200 -t 5 -x true


The output file consists of detected peaks. Each row(peak) has 7 columns as follows:

chromosome No.		start(bp)		stop(bp)		length of peak		volume of peak		maximum height of the peak		location of summit of the peak(bp)

