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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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  ~  This program is distributed in the hope that it will be useful,
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<jsap>
    <parameters>
        <unflaggedOption>
            <id>input</id>
            <required>true</required>
            <greedy>true</greedy>
            <help>The input filenames/basenames to to get statistics for. Compact file formats are recognized (reads or
                alignments).
            </help>
            <stringParser>
                <classname>FileStringParser</classname>
            </stringParser>
        </unflaggedOption>
        <flaggedOption>
            <id>output</id>
            <shortFlag>o</shortFlag>
            <longFlag>output</longFlag>
            <required>false</required>
            <help>Where the output will be written. If not specified, output will be written to stdout.</help>
        </flaggedOption>
        <flaggedOption>
            <id>type</id>
            <shortFlag>t</shortFlag>
            <longFlag>type</longFlag>
            <required>false</required>
            <help>The type of input, alignment or reads. Can be determined automatically from filenames, but useful when
                reading from stdin.
            </help>
        </flaggedOption>
        <flaggedOption>
            <id>number-of-quantiles</id>
            <shortFlag>q</shortFlag>
            <longFlag>number-of-quantiles</longFlag>
            <required>false</required>
            <help>Number of quantiles used to characterize read length distribution.</help>
            <stringParser>
                <classname>IntegerStringParser</classname>
            </stringParser>
        </flaggedOption>
        <switch>
            <id>verbose</id>
            <shortFlag>v</shortFlag>
            <longFlag>verbose</longFlag>
            <help>Display detailed statistics.</help>
        </switch>
        <switch>
                    <id>header-only</id>
                    <longFlag>header-only</longFlag>
                    <help>Only displays statistics from alignment headers (i.e, does not scan entries, tmh or other files).</help>
                </switch>
    </parameters>
</jsap>
