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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/daligner">Debian Med / daligner</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/daligner/-/commit/02bb795fe643ed8788eba5147924c38e3c972403">02bb795f</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-08-10T16:01:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0+git20200727.ed40ce5</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#c124e8106a395bb51daed9617fbfdbd81bb1165d">
LAsort.c
</a>
</li>
<li class="file-stats">
<a href="#ed8961b98ef7f44b09739544a4d58e3fffed0cda">
daligner.c
</a>
</li>
<li class="file-stats">
<a href="#3c41fd34a6f6633d79f03c873c93a1b2fe6e12cd">
filter.c
</a>
</li>
<li class="file-stats">
<a href="#84e6c9c4402c828fb5656ef01885adab758a29ca">
filter.h
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="c124e8106a395bb51daed9617fbfdbd81bb1165d">
<a href="https://salsa.debian.org/med-team/daligner/-/commit/02bb795fe643ed8788eba5147924c38e3c972403#c124e8106a395bb51daed9617fbfdbd81bb1165d"><strong>LAsort.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -284,10 +284,10 @@ int main(int argc, char *argv[])</td>
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<td class="diff-line-num old_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
284
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="c"> <span class="n" style="color: #333;">exit</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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285
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<td class="diff-line-num new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c"></span>
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<td class="diff-line-num old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
286
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<td class="diff-line-num new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fwrite</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">novl</span><span class="p">,</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">int64</span><span class="p">),</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">foutput</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
287
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<td class="diff-line-num new_line old" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="c"> <span class="n" style="color: #333;">SYSTEM_<span class="idiff left right">READ</span>_ERROR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="c"> <span class="n" style="color: #333;">SYSTEM_<span class="idiff left right">WRITE</span>_ERROR</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
288
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<td class="diff-line-num new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fwrite</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tspace</span><span class="p">,</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">foutput</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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289
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<td class="diff-line-num new_line old" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC289" class="line" lang="c"> <span class="n" style="color: #333;">SYSTEM_<span class="idiff left right">READ</span>_ERROR</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
290
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<td class="diff-line-num new_line old" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="c"> <span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="c"> <span class="n" style="color: #333;">SYSTEM_<span class="idiff left right">WRITE</span>_ERROR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="c"> </span>
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291
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">isize</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
292
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<td class="diff-line-num new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="c"> <span class="p">{</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iblock</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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293
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<td class="diff-line-num new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="c"> <span class="n" style="color: #333;">iblock</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Malloc</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ptrsize</span><span class="p">,</span><span class="s" style="color: #d14;">"Allocating LAsort input block"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -309,6 +309,11 @@ int main(int argc, char *argv[])</td>
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309
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="c"> <span class="p">}</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">novl</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">foutput</span><span class="p">);</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="c"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="c"> <span class="p">}</span></span>
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="c"> </span>
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313
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Set up unsorted permutation array</span></span>
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314
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -337,7 +342,7 @@ int main(int argc, char *argv[])</td>
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337
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="c"> <span class="n" style="color: #333;">sov</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">novl</span><span class="p">;</span></span>
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338
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="c"> <span class="p">}</span></span>
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Sort permutation array of ptrs to records</span></span>
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="c"> <span class="n" style="color: #333;">IBLOCK</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iblock</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -370,7 +375,9 @@ int main(int argc, char *argv[])</td>
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370
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="c"> <span class="n" style="color: #333;">fptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fblock</span><span class="p">;</span></span>
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371
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="c"> <span class="p">}</span></span>
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">equal</span><span class="p">)</span></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="c"> <span class="n" style="color: #333;">fptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">ovlsize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tsize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">fptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">ovlsize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tsize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="c"> <span class="n" style="color: #333;">novl</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">memmove</span><span class="p">(</span><span class="n" style="color: #333;">fptr</span><span class="p">,((</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">w</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ptrsize</span><span class="p">,</span><span class="n" style="color: #333;">ovlsize</span><span class="p">);</span></span>
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376
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="c"> <span class="n" style="color: #333;">fptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ovlsize</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -388,12 +395,15 @@ int main(int argc, char *argv[])</td>
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388
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="c"> <span class="p">}</span></span>
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389
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="c"> <span class="p">}</span></span>
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390
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="c"></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="c"> <span class="n" style="color: #333;">rewind</span><span class="p">(</span><span class="n" style="color: #333;">foutput</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fwrite</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">novl</span><span class="p">,</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">int64</span><span class="p">),</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">foutput</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="c"> <span class="n" style="color: #333;">SYSTEM_WRITE_ERROR</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="c"></span>
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391
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">perm</span><span class="p">);</span></span>
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392
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">foutput</span><span class="p">);</span></span>
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393
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="c"> <span class="p">}</span></span>
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394
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="c"> <span class="n" style="color: #333;">Free_Block_Arg</span><span class="p">(</span><span class="n" style="color: #333;">parse</span><span class="p">);</span></span>
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395
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="c"> <span class="p">}</span></span>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="c"></span>
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397
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="c"> </span>
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398
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iblock</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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399
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">iblock</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ptrsize</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/daligner/-/commit/02bb795fe643ed8788eba5147924c38e3c972403#ed8961b98ef7f44b09739544a4d58e3fffed0cda"><strong>daligner.c</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,6 +40,7 @@</td>
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40
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/types.h></span></span>
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41
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/stat.h></span></span>
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42
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <dirent.h></span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/resource.h></span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/param.h></span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if defined(BSD)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -470,6 +471,12 @@ int main(int argc, char *argv[])</td>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">NTHREADS</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">MAP_ORDER</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef PROFILE</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">rusage</span> <span class="n" style="color: #333;">stime</span><span class="p">,</span> <span class="n" style="color: #333;">etime</span><span class="p">;</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="c"> <span class="n" style="color: #333;">getrusage</span><span class="p">(</span><span class="n" style="color: #333;">RUSAGE_SELF</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stime</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="c"> <span class="p">{</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flags</span><span class="p">[</span><span class="mi" style="color: #099;">128</span><span class="p">];</span></span>
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482
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eptr</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -728,7 +735,24 @@ int main(int argc, char *argv[])</td>
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="c"> <span class="n" style="color: #333;">Close_DB</span><span class="p">(</span><span class="n" style="color: #333;">ablock</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">apath</span><span class="p">);</span></span>
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737
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">aroot</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="c"> <span class="n" style="color: #333;">Clean_Exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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738
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef PROFILE</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">int64</span> <span class="n" style="color: #333;">secs</span><span class="p">,</span> <span class="n" style="color: #333;">mics</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="c"> <span class="n" style="color: #333;">getrusage</span><span class="p">(</span><span class="n" style="color: #333;">RUSAGE_SELF</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">etime</span><span class="p">);</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="c"></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="c"> <span class="n" style="color: #333;">secs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">etime</span><span class="p">.</span><span class="n" style="color: #333;">ru_utime</span><span class="p">.</span><span class="n" style="color: #333;">tv_sec</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">stime</span><span class="p">.</span><span class="n" style="color: #333;">ru_utime</span><span class="p">.</span><span class="n" style="color: #333;">tv_sec</span><span class="p">;</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="c"> <span class="n" style="color: #333;">mics</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">etime</span><span class="p">.</span><span class="n" style="color: #333;">ru_utime</span><span class="p">.</span><span class="n" style="color: #333;">tv_usec</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">stime</span><span class="p">.</span><span class="n" style="color: #333;">ru_utime</span><span class="p">.</span><span class="n" style="color: #333;">tv_usec</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="c"> <span class="n" style="color: #333;">mics</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1000000</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">secs</span><span class="p">;</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="c"></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="c"> <span class="n" style="color: #333;">secs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">etime</span><span class="p">.</span><span class="n" style="color: #333;">ru_stime</span><span class="p">.</span><span class="n" style="color: #333;">tv_sec</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">stime</span><span class="p">.</span><span class="n" style="color: #333;">ru_stime</span><span class="p">.</span><span class="n" style="color: #333;">tv_sec</span><span class="p">;</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="c"> <span class="n" style="color: #333;">mics</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">etime</span><span class="p">.</span><span class="n" style="color: #333;">ru_stime</span><span class="p">.</span><span class="n" style="color: #333;">tv_usec</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">stime</span><span class="p">.</span><span class="n" style="color: #333;">ru_stime</span><span class="p">.</span><span class="n" style="color: #333;">tv_usec</span><span class="p">;</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="c"> <span class="n" style="color: #333;">mics</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1000000</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">secs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"T %lld</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">mics</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1000</span><span class="p">);</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="c"> <span class="n" style="color: #333;">Clean_Exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="c"> <span class="n" style="color: #333;">exit</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/daligner/-/commit/02bb795fe643ed8788eba5147924c38e3c972403#3c41fd34a6f6633d79f03c873c93a1b2fe6e12cd"><strong>filter.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,7 +28,7 @@</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "filter.h"</span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "align.h"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"><span class="idiff left right">#undef PROFILE</span> // WHen running sensitivity trials, compute histogram of</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="idiff left right"> </span> <span class="c1" style="color: #998; font-style: italic;">// WHen running sensitivity trials, compute histogram of</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAXHIT 1000 // false & true positive hit scores</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Debug Controls</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2521,7 +2521,7 @@ void Match_Filter(char *aname, DAZZ_DB *ablock, char *bname, DAZZ_DB *bblock,</td>
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2521
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2521
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<pre style="margin: 0;"> <span id="LC2521" class="line" lang="c"> <span class="p">}</span></span>
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2522
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2522
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<pre style="margin: 0;"> <span id="LC2522" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2523
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2523
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<pre style="margin: 0;"> <span id="LC2523" class="line" lang="c"></span>
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2524
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<pre style="margin: 0;">-<span id="LC2524" class="line" lang="c"> <span class="p">{</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_diag</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">ablock</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxlen</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">Binshift</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">((</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bblock</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxlen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">Binshift</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2524" class="line" lang="c"> <span class="p">{</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_diag</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">ablock</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxlen</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">Binshift</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">((</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bblock</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxlen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">Binshift</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;"><span class="idiff left right">3</span></span><span class="p">;</span></span>
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2525
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2525
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<pre style="margin: 0;"> <span id="LC2525" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">space</span><span class="p">;</span></span>
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2526
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2526
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<pre style="margin: 0;"> <span id="LC2526" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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2527
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2527
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<pre style="margin: 0;"> <span id="LC2527" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2556,7 +2556,7 @@ void Match_Filter(char *aname, DAZZ_DB *ablock, char *bname, DAZZ_DB *bblock,</td>
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2556
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2556
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<pre style="margin: 0;"> <span id="LC2556" class="line" lang="c"> <span class="n" style="color: #333;">space</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2557
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2557
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<pre style="margin: 0;"> <span id="LC2557" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">NTHREADS</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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2558
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2558
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<pre style="margin: 0;"> <span id="LC2558" class="line" lang="c"> <span class="p">{</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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2559
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<pre style="margin: 0;">-<span id="LC2559" class="line" lang="c"> <span class="n" style="color: #333;">parmr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">space</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">((</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="n" style="color: #333;"><span class="idiff">bblock</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">maxlen</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Binshift</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2559" class="line" lang="c"> <span class="n" style="color: #333;">parmr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">space</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">((<span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">bblock</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">maxlen</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Binshift</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">);</span></span>
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2560
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<pre style="margin: 0;"> <span id="LC2560" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2561
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2561
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<pre style="margin: 0;"> <span id="LC2561" class="line" lang="c"> <span class="n" style="color: #333;">parmr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parmr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">lasta</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">max_diag</span><span class="p">;</span></span>
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2562
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2562
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<pre style="margin: 0;"> <span id="LC2562" class="line" lang="c"> <span class="n" style="color: #333;">parmr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">lastp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parmr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">max_diag</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/daligner/-/commit/02bb795fe643ed8788eba5147924c38e3c972403#84e6c9c4402c828fb5656ef01885adab758a29ca"><strong>filter.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,8 @@</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "DB.h"</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "align.h"</span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#undef PROFILE</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"></span>
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17
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">VERBOSE</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -v flag is set?</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">MINOVER</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// minimum overlap (-l)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">HGAP_MIN</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// HGap minimum (-H)</span></span>
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