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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.
~
~ 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>
<unflaggedOption>
<id>input-basename</id>
<required>true</required>
<help>The compact alignment file to read as input.</help>
</unflaggedOption>
<flaggedOption>
<id>output</id>
<shortFlag>o</shortFlag>
<longFlag>output</longFlag>
<required>true</required>
<help>The SAM/BAM output file to output to. Please note that if the file ends in .bam, a BAM file will be
written, whereas if the file ends in .sam, a SAM file will be written instead.
</help>
</flaggedOption>
<flaggedOption>
<id>genome</id>
<shortFlag>g</shortFlag>
<longFlag>genome</longFlag>
<required>true</required>
<help>
The input genome in either 'compact random-access-genome' format or 'fa + fa.fai' format.
The random-access-genome file can be made from a fasta reference using the build-sequence-cache mode.
If using the random-access-genome input, specify any one of the files in the random-access-genome.
If using the '.fa + .fa.fai' input, specify the '.fa' file but make sure the '.fa.fai' file
is located in the same directory.
Using the random-access-genome format can be considerably faster, but uses more memory than using
the picard indexed fasta file.
</help>
</flaggedOption>
<flaggedOption>
<id>include-reference-names</id>
<shortFlag>r</shortFlag>
<longFlag>include-reference-names</longFlag>
<required>false</required>
<help>When provided, only process 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>
<flaggedOption>
<id>quality-encoding</id>
<longFlag>quality-encoding</longFlag>
<required>false</required>
<defaults>
<string>Phred</string>
</defaults>
<help>The encoding for quality scores. The default quality encoding is set to Sanger as per BAM/SAM
specification v1.4-r985. Valid encodings include Illumina, Sanger and Solexa.
</help>
</flaggedOption>
</parameters>
</jsap>
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