
-- DESCRIPTION --

   USAGE:
    appRepeats [options]  <reference>  <query>  <seeds>

    [options]    type 'appRepeats -h' for a list of options.
    <reference>  reference file with one or more FastA sequences
    <query>      query file with one or more FastA sequences
    <seeds>      a regular text file with the spaced seeds separated by newline

   OUTPUT:
                stdout  a list of approximate matches with their length and score

-- INSTALLATION --

After extracting the files into the desired installation directory,
change to this directory and type: "make"

This command will build the "appRepeats" binary. 

For sanity test, please execute the binary on the example files provided. 
On success, the script will print 2 detected repeats as output.


-- RUNNING --

The valid set of options for the program are:
Options:
Options:
	-n	match only the characters a, c, g, or t
  		they can be in upper or in lower case
	-L	set the minimum length of a match. The default length
  		is the length of the shortest seed
	-s	set the scoring matrix [Match,Mismatch,Indel]:
  			The default is [   2 ,   -2   ,  -3 ]
  			Usage:      -s  <int>  <int>  <int>
	-D	set the maximum edit distance between two matches.
  		The default distance is 5
	-x	set the Xdrop threshold score. The default is 5
	-e	set the E-value threshold. The default is 10
	-b	compute forward and reverse complement matches
	-r	only compute reverse complement matches
	-c	report the query-position of a reverse complement match
  		relative to the original query sequence
	-o	print output in file
	-f	force printing the reference sequence name beside each pair
  		regardless of the number of reference sequence input
	-l	show the length of the query sequences on the header line
	-k	set the step size for indexing the two sequences.
  		The default step is 1
	-d	set the split size. The default value is 1
	-t	number of threads. The default is 1 thread
	-h	show possible options
