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  ~ Copyright (C) 2009-2011 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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  ~  This program is distributed in the hope that it will be useful,
  ~  but WITHOUT ANY WARRANTY; without even the implied warranty of
  ~  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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<jsap>
    <parameters>
        <flaggedOption>
            <id>output</id>
            <shortFlag>o</shortFlag>
            <longFlag>output</longFlag>
            <required>false</required>
            <help>The output filename.</help>
        </flaggedOption>
        <flaggedOption>
            <id>chromosome-prefix</id>
            <longFlag>chromosome-prefix</longFlag>
            <required>false</required>
            <help>A prefix to append to chromsome names (e.g., +chr) or to remove (e.g., -chr).</help>
        </flaggedOption>
        <flaggedOption>
            <id>genome</id>
            <longFlag>genome</longFlag>
            <required>true</required>
            <help>A genome basename. The genome must have been processed by build-sequence-cache mode to produce the
                compressed, random access files this mode needs.
            </help>
        </flaggedOption>
        <unflaggedOption>
            <id>vcfInput</id>
            <required>true</required>
            <greedy>false</greedy>
            <help>The basenames of the input VCF files to compare.</help>
        </unflaggedOption>
    </parameters>
</jsap>
