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<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>
