fasta \
  -o hemi_pileup.bed \
  --log modkit.log
</code></pre>
<p>Many of the <code>pileup</code> options are available in <code>pileup-hemi</code> with a couple differences: :</p>
<ol>
<li>A motif must be provided. The <code>--cpg</code> flag is a preset to aggregate CpG hemi-methylation patterns as shown above.
If a motif is provided (as an argument to <code>--motif</code>) it must be reverse-complement palindromic.</li>
<li>A reference must be provided.</li>
<li>Both the positive strand base modificatio