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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.
~
~ 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>output</id>
<shortFlag>o</shortFlag>
<longFlag>output</longFlag>
<required>false</required>
<help>Where the sequence variations will be written.</help>
</flaggedOption>
<flaggedOption>
<id>format</id>
<shortFlag>f</shortFlag>
<longFlag>format</longFlag>
<required>false</required>
<defaults>
<string>tsv</string>
</defaults>
<help>Format of the output file (tsv).</help>
</flaggedOption>
<unflaggedOption>
<id>input</id>
<required>true</required>
<greedy>true</greedy>
<help>The basenames of input alignments.</help>
</unflaggedOption>
<flaggedOption>
<id>include-reference-names</id>
<shortFlag>r</shortFlag>
<longFlag>include-reference-names</longFlag>
<required>false</required>
<help>When provided, only process the reference identifiers listed in this comma separated list. To process only chromosome 19 and 1, if sequences are identified by "1" and "19", use: --include-reference-names 1,19 </help>
</flaggedOption>
</parameters>
</jsap>
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