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== Sequence Representation Parameters ==
== Sequence Representation Parameters (<code>--seqOrig</code>, <code>--seqBases</code>, <code>--seqEquals</code>) ==
The sequence parameters options specify how to represent the sequence if the reference is specified (refFile option). If the reference is not specified or seqOrig is specified, no modifications are made to the sequence. If the reference and seqBases is specified, any matches between the sequence and the reference are represented in the sequence as the appropriate base. If the reference and seqEquals is specified, any matches between the sequence and the reference are represented in the sequence as '='.
The sequence parameters options specify how to represent the sequence if the reference is specified (refFile option).
If the reference is not specified or seqOrig is specified, no modifications are made to the sequence.
If the reference and seqBases is specified, any matches between the sequence and the reference are represented in the sequence as the appropriate base.
If the reference and seqEquals is specified, any matches between the sequence and the reference are represented in the sequence as '='.
=== Examples ===
=== Examples ===
