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3.1 How to run qod

The format for running the qod command line program is: 

     qod [Options] <files...>
     
     qod --help|-h
Mandatory arguments to long options are mandatory for short options too. Options must appears in the order of their description below.

--help|-h Display the help message, then exit.
--full-version|-V Display complete version header.
--verbose|-v Display additional informations.
--quiet|-q Turn off warnings.
--tabular|-t Tabularize the output.
--axt|-x Use this if input alignment files follow the axt format.
--ref-seq|-f <file> Set the central genome sequence from file <file> (fasta –eventually gzipped– formatted).
--annotations|-a <file> Read annotation of the compared genome sequence in file <file> (sequin –eventually gzipped– formatted).
<files...> The <files...> should contain the description of pairwise local similarities.
Each file should contain the pairwise local similarities between the central genome and a given related genome. The files can be gzipped and must either follow the axt format (if option --axt is provided) or formatted as follow: 
       #Header
       #W_1
       [a_1,b_1] [c_1,d_1]
       ⋮
     
       #W_n
       [a_n,b_n] [c_n,d_n]

where W_i is the weight of the i^th interval, beginning at position a_i and ending at position b_i on the central genome sequence, and matching segment beginning at position \min(c_i, d_i) and ending at position \max(c_i,d_i) on the compared sequence. If c_i is greater than d_i, then the match occurs on the reverse complement of the compared sequence.