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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.
  ~
  ~  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
  ~  GNU General Public License for more details.
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  ~  You should have received a copy of the GNU General Public License
  ~  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  -->

<jsap>
    <parameters>

        <flaggedOption>
            <id>input</id>
            <shortFlag>i</shortFlag>
            <longFlag>input</longFlag>
            <stringParser>
                <classname>StringStringParser</classname>
            </stringParser>
            <required>true</required>
            <help>Name of the compact reads input file.</help>
        </flaggedOption>
        <flaggedOption>
            <id>output</id>
            <shortFlag>o</shortFlag>
            <longFlag>output</longFlag>
            <stringParser>
                <classname>StringStringParser</classname>
            </stringParser>
            <required>true</required>
            <help>Name of the compact reads output file. Sequences will be written to this output after bisulfite conversion (C->T).</help>
        </flaggedOption>
        <flaggedOption>
            <id>sequence-per-chunk</id>
            <shortFlag>n</shortFlag>
            <longFlag>sequence-per-chunk</longFlag>
            <stringParser>
                <classname>IntegerStringParser</classname>
            </stringParser>
            <required>false</required>
            <defaults>
                <string>10000</string>
            </defaults>
            <help>The number of sequences that will be written in each compressed chunk. Default is suitable for very many short sequences. Reduce to a few sequences per chunk if each sequence is very large.</help>
        </flaggedOption>
    </parameters>
</jsap>
