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  ~ Copyright (C) 2009-2010 Institute for Computational Biomedicine,
  ~                    Weill Medical College of Cornell University
  ~
  ~  This program is free software; you can redistribute it and/or modify
  ~  it under the terms of the GNU General Public License as published by
  ~  the Free Software Foundation; either version 3 of the License, or
  ~  (at your option) any later version.
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<jsap>
    <parameters>
        <unflaggedOption>
            <id>input</id>
            <required>true</required>
            <greedy>true</greedy>
            <help>The compact alignment file(s) to read as input.</help>
        </unflaggedOption>
        <flaggedOption>
            <id>output</id>
            <shortFlag>o</shortFlag>
            <longFlag>output</longFlag>
            <required>false</required>
            <help>The file where to write the inferred sex information.</help>
        </flaggedOption>

    </parameters>
</jsap>
