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By default reads that overlap the specified region are written. If instead you only want to write reads that are fully within the specified regions, use the <code>--withinReg</code> option.
=== Only Print Reads with a Specified Read Name (code>--readName</code>) ===
If you only want to print reads with a specific read name, use the <code>--readName</code> option followed by the read name.