<p>This is a bug pattern that seems to be in many places in phast:</p>
<pre><code>char c;
...
while ((c = (char)getopt_long(argc, argv, "i:o:s:e:l:G:r:T:a:g:c:C:L:I:A:M:O:w:N:Y:X:fuDVxPzRSk4mh", long_opts, &opt_idx)) != -1) {

</code></pre>
<p>The casts in commit <a class="commit-link" data-hovercard-type="commit" data-hovercard-url="https://github.com/CshlSiepelLab/phast/commit/273b8ce677e1e57f5c2aa5309f9b6dff319b4a03/hovercard" href="https://github.com/CshlSiepelLab/phast/commit/273b8ce677e1e57f5c2aa5309f9b6dff319b4a03"><tt>273b8ce</tt></a> silenced the warnings where the compiler was warning about this bug...</p>

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