# This file is not used anywhere. It just lists some the command-line arguments to oligowalk for debugging purposes.

"-seq" => input sequnce file
## "-o" => reportfilename //output file stored the result in debug mode
## "-m" =>choice of mode, see detatil at the beginning of main function
## next-int

## "-st" => start position of folding region of target
start = next-int

## "-en" end = ##next-int

## "-M" => start posion of scanning on folded region of target
M = next-int

## "-N")){
N = next-int

## "-l" =>length of hybridiztion
length = next-int

## "-type" =>if it is a DNA or RNA
if(!strcmp(argv[i+1],"d"))	isdna=true;

## "-s" =>suboptimal structure choices
suboptimal = next-int

## "-co" =>concentration of oligo
conc = next-int

## "-unit" =>concentration of oligo
unit = next-int

## "-fi" =>prefilter of siRNA
useprefilter = next-int

## "-score" =>prefilter of siRNA
scoreit = true; 

## "-fold" =>fold substructure size centered on binding
foldsize = next-int

## "-dist" =>fold substructure size centered on binding
distance = next-int

## "-shape" =>fold substructure size centered on binding
shapefile = next-arg

## "-test" =>fold substructure size centered on binding
TESTnum = next-int

for (j=1;j<=TESTnum;j++)		TESTon[j]=atoi(argv[i+1+j]);
	i=i+2+TESTnum;
}
## "-write" =>write sav files to save time in test mode
WRITE= true;