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  ~                    Weill Medical College of Cornell University
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<jsap>
    <parameters>
        <flaggedOption>
            <id>output</id>
            <shortFlag>o</shortFlag>
            <longFlag>output</longFlag>
            <required>true</required>
            <help>The output filename to write the merged alignments to.</help>
        </flaggedOption>
        <flaggedOption>
            <id>k</id>
            <shortFlag>k</shortFlag>
            <longFlag>k</longFlag>
            <required>false</required>
            <stringParser>
                <classname>IntegerStringParser</classname>
            </stringParser>
            <defaults>
                <string>[K_VALUE]</string>
            </defaults>
            <help>The k values for the merge.  If gene-transcript-map-file is defined, the alignment was against transcripts. k defines the maximum number of genes that a read may match. Best value is probably 1.  If gene-transcript-map-file is NOT defined, the alignment was against a reference genome. k defines the maximum number of duplicates allowed for the top quality score when there are duplicates.  </help>
        </flaggedOption>
       <switch>
            <id>hi-c</id>
            <longFlag>hi-c</longFlag>
            <help>When this switch is provided, use a merge strategy suitable for hi-c alignments. The strategy works with exactly two input files, which must have been sequenced as pair in the Hi-C protocol.</help>
        </switch>
        <flaggedOption>
            <id>gene-transcript-map-file</id>
            <shortFlag>g</shortFlag>
            <longFlag>gene-transcript-map-file</longFlag>
            <required>false</required>
            <help>A TSV file that specifies the gene-transcript mapping.</help>
        </flaggedOption>
        <unflaggedOption>
            <id>input</id>
            <required>true</required>
            <greedy>true</greedy>
            <help>The input alignment files to merge.</help>
        </unflaggedOption>
    </parameters>
</jsap>
