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<h3 style="margin-top: 20px; margin-bottom: 10px;">

Andreas Tille pushed to branch master at <a href="https://salsa.debian.org/med-team/proteinortho" style="color: #1068bf;">Debian Med / proteinortho</a>

</h3>

<h4 style="margin-top: 10px; margin-bottom: 10px;">

Commits:

</h4>

<ul>

<li>

<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/24cd3c07a72436e375ad6056d13fae474ae5355f" style="color: #1068bf;">24cd3c07</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2022-11-26T06:28:27+01:00 </i>

</div>

<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Fix watch file

</pre>

</li>

<li>

<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/bec02a9cc4de4b0c37f4ac73bf7231decc076394" style="color: #1068bf;">bec02a9c</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2022-11-26T06:28:54+01:00 </i>

</div>

<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>New upstream version 6.1.4+dfsg</pre>

</li>

<li>

<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3f615c18988bd95b1bbeb57f75b567280e947972" style="color: #1068bf;">3f615c18</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2022-11-26T06:28:54+01:00 </i>

</div>

<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>routine-update: New upstream version

</pre>

</li>

<li>

<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/9acfc5be3d5e52b252c2e45c25c691baeda66b17" style="color: #1068bf;">9acfc5be</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2022-11-26T06:28:54+01:00 </i>

</div>

<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Update upstream source from tag 'upstream/6.1.4+dfsg'

Update to upstream version '6.1.4+dfsg'

with Debian dir a2621cec7bbd46d26e3d676155a87a14b4b73fb9</pre>

</li>

<li>

<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/85c9aa9ec8f6a1e761239bffa81ccefe3ba3779a" style="color: #1068bf;">85c9aa9e</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2022-11-26T06:31:44+01:00 </i>

</div>

<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4 style="margin-top: 10px; margin-bottom: 10px;">

9 changed files:

</h4>

<ul>

<li class="file-stats">

<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a" style="color: #1068bf;">

CHANGELOG

</a>

</li>

<li class="file-stats">

<a href="#ff6936350384213d6f693f4d604134188ce088c8" style="color: #1068bf;">

CHANGEUID

</a>

</li>

<li class="file-stats">

<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c" style="color: #1068bf;">

Makefile

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1" style="color: #1068bf;">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79" style="color: #1068bf;">

debian/watch

</a>

</li>

<li class="file-stats">

<a href="#c9e37a96ac72f9ef076d7a41a57470524d63b36e" style="color: #1068bf;">

proteinortho6.pl

</a>

</li>

<li class="file-stats">

<a href="#9fa949bc0321e9cba9ff960eb0439ff00683ae89" style="color: #1068bf;">

src/po_tree.c

</a>

</li>

<li class="file-stats">

<a href="#ba368ee46e511166051985e745eaa37aea49d150" style="color: #1068bf;">

src/proteinortho_clustering.cpp

</a>

</li>

<li class="file-stats">

<a href="#1486be463578edbd60b13d54cd9e0d2b9d4ecd99" style="color: #1068bf;">

src/proteinortho_summary.pl

</a>

</li>

</ul>

<h4 style="margin-top: 10px; margin-bottom: 10px;">

Changes:

</h4>

<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/427c970d6dc7f60f2e664a405045ea9af4a8fe2e...85c9aa9ec8f6a1e761239bffa81ccefe3ba3779a#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a" style="color: #1068bf;"><strong style="font-weight: bold;">CHANGELOG</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -364,4 +364,15 @@</td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

364

</td>

<td class="new_line diff-line-num" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

364

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC364" class="line" lang="plaintext">            - new: automatic prurity detetection (proteinortho_clustering)</span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

365

</td>

<td class="new_line diff-line-num" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

365

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC365" class="line" lang="plaintext">            - BUGFIX: remove.graph was missing edges removed from purity</span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

366

</td>

<td class="new_line diff-line-num" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

366

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC366" class="line" lang="plaintext">    24. Okt (6041) v6.1.2</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

367

</td>

<td class="new_line diff-line-num old" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC367" class="line" lang="plaintext">            - BUGFIX: proteinortho2html some times got the , wrong in the pop-up window.</span></pre></td>

</tr>

<tr class="line_holder old-nonewline" style="line-height: 1.6;">

<td class="old_line diff-line-num" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa"></td>

<td class="new_line diff-line-num" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa"></td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">\ No newline at end of file</td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

367

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC367" class="line" lang="plaintext">            - BUGFIX: proteinortho2html some times got the , wrong in the pop-up window.</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

368

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC368" class="line" lang="plaintext">    4. Nov (6042) v6.1.3</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

369

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC369" class="line" lang="plaintext">            - small bugfix: when cleaning data on symlinks, the new "X_clean" files are generated in abs_path which may not be in the input directory! </span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

370

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC370" class="line" lang="plaintext">            - removed the precompiled proteinortho_treeBuilderCore as virustotal is not happy with this file (false positive hit: #65, thanks to Björn for pointing this out)</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

371

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC371" class="line" lang="plaintext">            - small bugfix: subparaBlast with diamond and e.g. fast did not work previously</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

372

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC372" class="line" lang="plaintext">    15. Nov (6045) v6.1.3</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

373

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC373" class="line" lang="plaintext">            - small adjustments to the upper limit of the automatic purity detection system (0.1 -> 0.12)</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

374

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC374" class="line" lang="plaintext">            - added the with and without lapack test back to the Makefile (make test or make test_step3)</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

375

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC375" class="line" lang="plaintext">            - refined feature for proteinortho_clustering -maxnodes: if max-nodes are exceeded, remove the worst 10% of edges of this CC (by weight) until the CC breaks into smaller CC</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

376

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC376" class="line" lang="plaintext">    23. Nov (6051) v6.1.4</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

377

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC377" class="line" lang="plaintext">            - small bugfix: newlines of the output of proteinortho_summary.pl are now printed to STDOUT instead of STDERR, thanks to Matthias Bernt</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

378

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC378" class="line" lang="plaintext">            - bugfix: for large project the step=1 could soft lock itself sometimes caused by the log_worker (if used with many cores)</span></pre></td>

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<br>

</li>

<li id="ff6936350384213d6f693f4d604134188ce088c8">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/427c970d6dc7f60f2e664a405045ea9af4a8fe2e...85c9aa9ec8f6a1e761239bffa81ccefe3ba3779a#ff6936350384213d6f693f4d604134188ce088c8" style="color: #1068bf;"><strong style="font-weight: bold;">CHANGEUID</strong></a>

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1

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<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1" class="line" lang="plaintext">60<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>1</span></pre></td>

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1" class="line" lang="plaintext">60<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>1</span></pre></td>

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</table>

<br>

</li>

<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/427c970d6dc7f60f2e664a405045ea9af4a8fe2e...85c9aa9ec8f6a1e761239bffa81ccefe3ba3779a#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c" style="color: #1068bf;"><strong style="font-weight: bold;">Makefile</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -96,7 +96,7 @@ endif</td>

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<td class="old_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

96

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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

96

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC96" class="line" lang="make"><span class="nv" style="color: #008080;">dir_guard</span><span class="o" style="font-weight: 600;">=</span>@if <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Creating build directory ..."</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

97

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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC97" class="line" lang="make"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

98

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<td class="new_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC98" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all</span></span>

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<td class="old_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

99

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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC99" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span><span class="nf" style="color: #900; font-weight: 600;">echoENV $(BUILDDIR)/proteinortho_extract_from_graph.pl $(BUILDDIR)/proteinortho_compareProteinorthoGraphs.pl $(BUILDDIR)/proteinortho_grab_proteins.pl $(BUILDDIR)/proteinortho_formatUsearch.pl $(BUILDDIR)/proteinortho_do_mcl.pl $(BUILDDIR)/proteinortho2tree.pl $(BUILDDIR)/proteinortho2html.pl $(BUILDDIR)/proteinortho2xml.pl $(BUILDDIR)/proteinortho_singletons.pl $(BUILDDIR)/proteinortho_summary.pl $(BUILDDIR)/proteinortho_ffadj_mcs.py $(BUILDDIR)/proteinortho_clustering $(BUILDDIR)/proteinortho_history.pl $(BUILDDIR)/proteinortho_graphMinusRemovegraph $(BUILDDIR)/proteinortho_cleanupblastgraph<span class="idiff left right deletion" style="background-color: #fac5cd;"> $(BUILDDIR)/proteinortho_treeBuilderCore</span></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

99

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC99" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span><span class="nf" style="color: #900; font-weight: 600;">echoENV $(BUILDDIR)/proteinortho_extract_from_graph.pl $(BUILDDIR)/proteinortho_compareProteinorthoGraphs.pl $(BUILDDIR)/proteinortho_grab_proteins.pl $(BUILDDIR)/proteinortho_formatUsearch.pl $(BUILDDIR)/proteinortho_do_mcl.pl $(BUILDDIR)/proteinortho2tree.pl $(BUILDDIR)/proteinortho2html.pl $(BUILDDIR)/proteinortho2xml.pl $(BUILDDIR)/proteinortho_singletons.pl $(BUILDDIR)/proteinortho_summary.pl $(BUILDDIR)/proteinortho_ffadj_mcs.py $(BUILDDIR)/proteinortho_clustering $(BUILDDIR)/proteinortho_history.pl $(BUILDDIR)/proteinortho_graphMinusRemovegraph $(BUILDDIR)/proteinortho_cleanupblastgraph</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

100

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<td class="new_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

100

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC100" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[100%] </span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">Everything is compiled with no errors.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

101

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<td class="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

101

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC101" class="line" lang="make"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

102

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<td class="new_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC102" class="line" lang="make"><span class="nl">$(BUILDDIR)/proteinortho_extract_from_graph.pl</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">src/proteinortho_extract_from_graph.pl</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -264,7 +264,7 @@ else</td>

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<td class="old_line diff-line-num" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

264

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<td class="new_line diff-line-num" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC264" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

265

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<td class="new_line diff-line-num" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

265

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC265" class="line" lang="make"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

266

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<td class="new_line diff-line-num" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC266" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">install</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

267

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<td class="new_line diff-line-num old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC267" class="line" lang="make"><span class="nl">install</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">proteinortho6.pl proteinortho $(BUILDDIR)/proteinortho_extract_from_graph.pl $(BUILDDIR)/proteinortho_formatUsearch.pl $(BUILDDIR)/proteinortho_compareProteinorthoGraphs.pl $(BUILDDIR)/proteinortho_do_mcl.pl $(BUILDDIR)/proteinortho2html.pl $(BUILDDIR)/proteinortho2xml.pl $(BUILDDIR)/proteinortho_clustering $(BUILDDIR)/proteinortho_singletons.pl $(BUILDDIR)/proteinortho_ffadj_mcs.py $(BUILDDIR)/proteinortho2tree.pl $(BUILDDIR)/proteinortho_history.pl $(BUILDDIR)/proteinortho_cleanupblastgraph $(BUILDDIR)/proteinortho_graphMinusRemovegraph <span class="idiff left right deletion" style="background-color: #fac5cd;">$(BUILDDIR)/proteinortho_treeBuilderCore </span>$(BUILDDIR)/proteinortho_grab_proteins.pl $(BUILDDIR)/proteinortho_summary.pl $(BUILDDIR)/proteinortho_history.pl </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC267" class="line" lang="make"><span class="nl">install</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">proteinortho6.pl proteinortho $(BUILDDIR)/proteinortho_extract_from_graph.pl $(BUILDDIR)/proteinortho_formatUsearch.pl $(BUILDDIR)/proteinortho_compareProteinorthoGraphs.pl $(BUILDDIR)/proteinortho_do_mcl.pl $(BUILDDIR)/proteinortho2html.pl $(BUILDDIR)/proteinortho2xml.pl $(BUILDDIR)/proteinortho_clustering $(BUILDDIR)/proteinortho_singletons.pl $(BUILDDIR)/proteinortho_ffadj_mcs.py $(BUILDDIR)/proteinortho2tree.pl $(BUILDDIR)/proteinortho_history.pl $(BUILDDIR)/proteinortho_cleanupblastgraph $(BUILDDIR)/proteinortho_graphMinusRemovegraph $(BUILDDIR)/proteinortho_grab_proteins.pl $(BUILDDIR)/proteinortho_summary.pl $(BUILDDIR)/proteinortho_history.pl </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

268

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<td class="new_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC268" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"INSTALLING everything to </span><span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="s2" style="color: #d14;">"</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

269

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<td class="new_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC269" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-v</span> <span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="p">;</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC270" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">Everything installed successfully to </span><span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="s2" style="color: #d14;">.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -390,22 +390,22 @@ test_step2: proteinortho6.pl</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC390" class="line" lang="make"><span class="nl">test_step3</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">proteinortho6.pl</span></span>

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<td class="new_line diff-line-num" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC391" class="line" lang="make"> ./proteinortho6.pl <span class="nt" style="color: #000080;">-silent</span> <span class="nt" style="color: #000080;">-force</span> <span class="nt" style="color: #000080;">-project</span><span class="o" style="font-weight: 600;">=</span>test_blastp <span class="nt" style="color: #000080;">-p</span><span class="o" style="font-weight: 600;">=</span>blastp <span class="nb" style="color: #0086b3;">test</span>/<span class="k" style="font-weight: 600;">*</span>.faa<span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC392" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[TEST] 2. -step=3 tests (proteinortho_clustering) "</span></span>

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<td class="old_line diff-line-num old" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC393" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" [1/<span class="idiff left right deletion" style="background-color: #fac5cd;">3</span>] various test functions of proteinortho_clustering (if this fails, try make clean first): "</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC393" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" [1/<span class="idiff left right addition" style="background-color: #c7f0d2;">4</span>] various test functions of proteinortho_clustering (if this fails, try make clean first): "</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

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<td class="new_line diff-line-num" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC394" class="line" lang="make"> <span class="nv" style="color: #008080;">OMP_NUM_THREADS</span><span class="o" style="font-weight: 600;">=</span>1 <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/proteinortho_clustering <span class="nt" style="color: #000080;">-test</span><span class="o" style="font-weight: 600;">></span> /dev/null 2>&1</span>

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<td class="new_line diff-line-num" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC395" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">passed</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span></span>

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<td class="old_line diff-line-num old" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC396" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" [2/<span class="idiff left right deletion" style="background-color: #fac5cd;">3</span>] Test proteinortho_clustering using lapack: "</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

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<td class="new_line diff-line-num old" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC397" class="line" lang="make"> <span class="nv" style="color: #008080;">OMP_NUM_THREADS</span><span class="o" style="font-weight: 600;">=</span>1 <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/proteinortho_clustering <span class="nt" style="color: #000080;">-lapack</span> 2 test_blastp.blast-graph <span class="nt" style="color: #000080;"><span class="idiff left deletion" style="background-color: #fac5cd;">-debug</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> 1 </span>2>test_lapack.err <span class="o" style="font-weight: 600;">></span>test_lapack.proteinortho.tsv <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC396" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" [2/<span class="idiff left right addition" style="background-color: #c7f0d2;">4</span>] Test proteinortho_clustering using lapack: "</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC397" class="line" lang="make"> <span class="nv" style="color: #008080;">OMP_NUM_THREADS</span><span class="o" style="font-weight: 600;">=</span>1 <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/proteinortho_clustering <span class="nt" style="color: #000080;">-lapack</span> 2 <span class="nt" style="color: #000080;"><span class="idiff left addition" style="background-color: #c7f0d2;">-debug</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> 1 </span>test_blastp.blast-graph 2>test_lapack.err <span class="o" style="font-weight: 600;">></span>test_lapack.proteinortho.tsv <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

398

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<td class="new_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC398" class="line" lang="make"> <span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span> <span class="p">;</span> ./src/chk_test.pl test_lapack.proteinortho.tsv<span class="p">;</span> </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

399

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<td class="new_line diff-line-num" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

399

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC399" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">passed</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

400

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<td class="new_line diff-line-num" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

400

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC400" class="line" lang="make"> <span class="p">@</span>perl <span class="nt" style="color: #000080;">-lne</span> <span class="s1" style="color: #d14;">'print join "\t", sort split("\t",$$_)'</span> remove.graph | <span class="nb" style="color: #0086b3;">sort</span> <span class="o" style="font-weight: 600;">></span> test.A<span class="p">;</span> </span>

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<td class="old_line diff-line-num old" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

401

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<td class="new_line diff-line-num old" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC401" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" [3/<span class="idiff left right deletion" style="background-color: #fac5cd;">3</span>] Test proteinortho_clustering using power: "</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

402

</td>

<td class="new_line diff-line-num old" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC402" class="line" lang="make"> <span class="nv" style="color: #008080;">OMP_NUM_THREADS</span><span class="o" style="font-weight: 600;">=</span>1 <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/proteinortho_clustering <span class="nt" style="color: #000080;">-lapack</span> 0 test_blastp.blast-graph <span class="nt" style="color: #000080;"><span class="idiff left deletion" style="background-color: #fac5cd;">-debug</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> 1 </span>2>test_power.err <span class="o" style="font-weight: 600;">></span>test_power.proteinortho.tsv<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

401

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC401" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" [3/<span class="idiff left right addition" style="background-color: #c7f0d2;">4</span>] Test proteinortho_clustering using power: "</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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402

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC402" class="line" lang="make"> <span class="nv" style="color: #008080;">OMP_NUM_THREADS</span><span class="o" style="font-weight: 600;">=</span>1 <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/proteinortho_clustering <span class="nt" style="color: #000080;">-lapack</span> 0 <span class="nt" style="color: #000080;"><span class="idiff left addition" style="background-color: #c7f0d2;">-debug</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> 1 </span>test_blastp.blast-graph 2>test_power.err <span class="o" style="font-weight: 600;">></span>test_power.proteinortho.tsv<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

403

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<td class="new_line diff-line-num" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC403" class="line" lang="make"> <span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span> <span class="p">;</span> ./src/chk_test.pl test_power.proteinortho.tsv<span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

404

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<td class="new_line diff-line-num" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

404

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC404" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">passed</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

405

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<td class="new_line diff-line-num old" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC405" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"><span class="idiff left right deletion" style="background-color: #fac5cd;">#</span>@perl -lne 'print join "</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">", sort split("</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">",</span><span class="nv" style="color: #008080;">$$</span><span class="s2" style="color: #d14;">_)' remove.graph | sort > test.B; </span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

406

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<td class="new_line diff-line-num old" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC406" class="line" lang="make"> <span class="s2" style="color: #d14;"><span class="idiff left right deletion" style="background-color: #fac5cd;">#</span>@echo -n "</span> <span class="o" style="font-weight: 600;">[</span>4/4] Test differences between <span class="s1" style="color: #d14;">'using lapack'</span> and <span class="s1" style="color: #d14;">'using power'</span>: <span class="s2" style="color: #d14;">"; </span><span class="se" style="color: #d14;">\</span></span>

</pre></td>

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407

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<td class="new_line diff-line-num old" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC407" class="line" lang="make"><span class="s2" style="color: #d14;"> <span class="idiff left right deletion" style="background-color: #fac5cd;">#</span>set -e ; diff test.A test.B;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

408

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<td class="new_line diff-line-num old" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC408" class="line" lang="make"> <span class="s2" style="color: #d14;"><span class="idiff left right deletion" style="background-color: #fac5cd;">#</span>@echo "</span><span class="nv" style="color: #008080;">$(GREEN)</span>passed<span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span></span>

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<td class="old_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

405

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC405" class="line" lang="make"> <span class="p">@</span>perl <span class="nt" style="color: #000080;">-lne</span> <span class="s1" style="color: #d14;">'print join "\t", sort split("\t",$$_)'</span> remove.graph | <span class="nb" style="color: #0086b3;">sort</span> <span class="o" style="font-weight: 600;">></span> test.B<span class="p">;</span> </span>

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<td class="old_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

406

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC406" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" [4/4] Test differences between 'using lapack' and 'using power': "</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

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<td class="old_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

407

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC407" class="line" lang="make"> <span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span> <span class="p">;</span> diff test.A test.B<span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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408

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC408" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">passed</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

409

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<td class="new_line diff-line-num" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC409" class="line" lang="make"></span>

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<td class="old_line diff-line-num" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

410

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<td class="new_line diff-line-num" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

410

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC410" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">test_step3_ring4_K5_power</span></span>

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<td class="old_line diff-line-num" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

411

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<td class="new_line diff-line-num" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

411

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC411" class="line" lang="make"><span class="nl">test_step3_ring4_K5_power</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">proteinortho6.pl</span></span>

</pre></td>

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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/427c970d6dc7f60f2e664a405045ea9af4a8fe2e...85c9aa9ec8f6a1e761239bffa81ccefe3ba3779a#9c96da0e9f91d7d8937b69b524702c106258f0d1" style="color: #1068bf;"><strong style="font-weight: bold;">debian/changelog</strong></a>

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1

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1" class="line" lang="plaintext">proteinortho (6.1.4+dfsg-1) unstable; urgency=medium</span>

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2

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2" class="line" lang="plaintext"></span>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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3

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3" class="line" lang="plaintext">  * Fix watch file</span>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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4

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC4" class="line" lang="plaintext">  * New upstream version</span>

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5

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC5" class="line" lang="plaintext"></span>

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6

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Sat, 26 Nov 2022 06:29:10 +0100</span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC7" class="line" lang="plaintext"></span>

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1

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" class="line" lang="plaintext">proteinortho (6.1.2+dfsg-1) unstable; urgency=medium</span>

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2

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

9

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="plaintext"></span>

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3

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC10" class="line" lang="plaintext">  [ Andreas Tille ]</span>

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</li>

<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/427c970d6dc7f60f2e664a405045ea9af4a8fe2e...85c9aa9ec8f6a1e761239bffa81ccefe3ba3779a#68ef9f98c01c7eecd4c605cc26048a06f3304b79" style="color: #1068bf;"><strong style="font-weight: bold;">debian/watch</strong></a>

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1

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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1" class="line" lang="plaintext">version=4</span>

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2

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2" class="line" lang="plaintext"></span>

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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

3

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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC3" class="line" lang="plaintext">opts="repacksuffix=+dfsg,dversionmangle=auto,<span class="idiff left right deletion" style="background-color: #fac5cd;">repack,compression=xz</span>" \</span>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

4

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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC4" class="line" lang="plaintext">  https://gitlab.com/paulklemm_PHD/proteinortho/tags?sort=updated_desc <span class="idiff left right deletion" style="background-color: #fac5cd;">.*/archive/</span>.*/proteinortho-v@ANY_VERSION@\.tar\.gz</span></pre></td>

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3" class="line" lang="plaintext">opts="repacksuffix=+dfsg,dversionmangle=auto,<span class="idiff left right addition" style="background-color: #c7f0d2;">filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%</span>" \</span>

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<td class="old_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC4" class="line" lang="plaintext">  https://gitlab.com/paulklemm_PHD/proteinortho/tags?sort=updated_desc .*/proteinortho-v@ANY_VERSION@\.tar\.gz</span></pre></td>

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<li id="c9e37a96ac72f9ef076d7a41a57470524d63b36e">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/427c970d6dc7f60f2e664a405045ea9af4a8fe2e...85c9aa9ec8f6a1e761239bffa81ccefe3ba3779a#c9e37a96ac72f9ef076d7a41a57470524d63b36e" style="color: #1068bf;"><strong style="font-weight: bold;">proteinortho6.pl</strong></a>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -509,7 +509,7 @@ use POSIX;</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC509" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC510" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Variables</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC511" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

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<td class="new_line diff-line-num old" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC512" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.1.<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span></span><span class="p">";</span></span>

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<td class="old_line diff-line-num new" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

512

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC512" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.1.<span class="idiff left right addition" style="background-color: #c7f0d2;">4</span></span><span class="p">";</span></span>

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<td class="old_line diff-line-num" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

513

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<td class="new_line diff-line-num" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC513" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span>    <span class="c1" style="color: #998; font-style: italic;"># 0/1/2/3 -> do all / only apply step 1 / only apply step 2 / only apply step 3</span></span>

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<td class="old_line diff-line-num" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

514

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<td class="new_line diff-line-num" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

514

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC514" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1   -> don't / be verbose</span></span>

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<td class="old_line diff-line-num" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

515

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<td class="new_line diff-line-num" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC515" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$core</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -705,6 +705,9 @@ foreach my $option (@ARGV) {</td>

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705

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<td class="new_line diff-line-num" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC705" class="line" lang="perl"><span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC706" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$inproject</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="nv" style="color: #008080;">$inproject</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$project</span><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;"># if --inproject is not specified then set it to --project</span></span>

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707

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<td class="new_line diff-line-num" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC707" class="line" lang="perl"></span>

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<td class="old_line diff-line-num new" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

708

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC708" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># for no input -> print usage </span></span>

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<td class="old_line diff-line-num new" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

709

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC709" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@ARGV</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">&print_header</span><span class="p">;</span><span class="nv" style="color: #008080;">print_usage_more</span><span class="p">();</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

710

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC710" class="line" lang="perl"></span>

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<td class="new_line diff-line-num" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

711

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC711" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$jobnumber</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$tmp_path</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""</span> <span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Please consider to use the -tmp option in combination with -jobs if you use proteinortho on a computing cluster system. Usually these clusters have dedicated local scratch directories.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

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712

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC712" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$selfblast</span><span class="p">){</span><span class="nv" style="color: #008080;">$checkblast</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="old_line diff-line-num" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

710

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<td class="new_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

713

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC713" class="line" lang="perl"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -943,7 +946,7 @@ if( $keep && $cpus > 8 ){ print STDERR "!!!$ORANGE\n[Warning]:$NC The '-keep' op</td>

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<td class="old_line diff-line-num" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

943

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<td class="new_line diff-line-num" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

946

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC946" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># 6.0.32 check if there are _clean files available -> use it instead. </span></span>

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<td class="old_line diff-line-num" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

944

</td>

<td class="new_line diff-line-num" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

947

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC947" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">search_clean_file</span><span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

945

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<td class="new_line diff-line-num" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

948

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC948" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

946

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<td class="new_line diff-line-num old" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC946" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file_clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;"><span class="idiff left deletion" style="background-color: #fac5cd;">abs_path</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> </span><span class="nv" style="color: #008080;">$file</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

949

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC949" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file_clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$file</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

947

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<td class="new_line diff-line-num" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

950

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC950" class="line" lang="perl">  <span class="nv" style="color: #008080;">$file_clean</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/(\.[^.]+)$/_clean$1/</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

948

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<td class="new_line diff-line-num" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

951

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC951" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$file_clean</span><span class="p">){</span><span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$file_clean</span><span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

949

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<td class="new_line diff-line-num" data-linenumber="952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

952

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC952" class="line" lang="perl">  <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$file</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -999,10 +1002,25 @@ if ($step == 0 || $step == 1) {</td>

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<td class="old_line diff-line-num" data-linenumber="999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

999

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<td class="new_line diff-line-num" data-linenumber="1002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1002

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1002" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$GREEN</span><span class="s2" style="color: #d14;">**Step 1**</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

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<td class="old_line diff-line-num" data-linenumber="1000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1000

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<td class="new_line diff-line-num" data-linenumber="1003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1003

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1003" class="line" lang="perl"></span>

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<td class="old_line diff-line-num" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1001

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<td class="new_line diff-line-num" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1004

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1004" class="line" lang="perl">  <span class="nv" style="color: #008080;">$do_log</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="old_line diff-line-num new" data-linenumber="1002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1005

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1005" class="line" lang="perl">  <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">kill</span><span class="p">('</span><span class="s1" style="color: #d14;">KILL</span><span class="p">')</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">detach</span> <span class="k" style="font-weight: 600;">foreach</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">();</span> </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1002

</td>

<td class="new_line diff-line-num" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1006

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1006" class="line" lang="perl">  <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">create</span><span class="p">('</span><span class="s1" style="color: #d14;">log_Worker</span><span class="p">');</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1003

</td>

<td class="new_line diff-line-num" data-linenumber="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1007

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1007" class="line" lang="perl">  <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$step1_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">enqueue</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">);</span> <span class="p">}</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1004

</td>

<td class="new_line diff-line-num old" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1004" class="line" lang="perl">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$cpus</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$debug</span> <span class="p">?</span> <span class="nv" style="color: #008080;">$cpus</span> <span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">create</span><span class="p">('</span><span class="s1" style="color: #d14;">generate_indices_Worker</span><span class="p">')</span> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;"># spawn a thread for each core</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1008

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1008" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Creating </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$cpus</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$debug</span> <span class="p">?</span> <span class="nv" style="color: #008080;">$cpus</span> <span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> generate_indices_Worker (cpus=</span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;">) for </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$step1_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> jobs</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1009

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1009" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">currently running </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">())</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> threads (pre spawn)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1010

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1010" class="line" lang="perl">  <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">create</span><span class="p">('</span><span class="s1" style="color: #d14;">generate_indices_Worker</span><span class="p">');</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1011

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1011" class="line" lang="perl">  </span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1012

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1012" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># INFO:</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1013

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1013" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># here we use only one thread to generate the db files !</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1014

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1014" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># -> diamond will fail if multiple makedb instances are running in parallel, </span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1015

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1015" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;">#    prducing un-joinable running threads (stuck within the `$cmd 2>&1` in the generate_indices)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1016

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1016" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># approx 1 in 10 runs fail with a infinte loop see issue #69 (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/69)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1017

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1017" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># work-around in 6.1.4</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1018

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1018" class="line" lang="perl">  </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1019

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1019" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># code for multiple threads (does not work sometimes for diamond): </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1020

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1020" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;">#for (my $i = 0; $i < ((scalar @files > 500 && scalar @files > $cpus+10) || $debug ? $cpus : 1) ; $i++) { my $tmp = threads->create('generate_indices_Worker') } # spawn a thread for each core</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1021

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1021" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">currently running </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">())</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> threads (post spawn)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1005

</td>

<td class="new_line diff-line-num" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1022

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1022" class="line" lang="perl">  <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">join</span><span class="p">()</span> <span class="k" style="font-weight: 600;">foreach</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">();</span> </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1023

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1023" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#  $_->kill('KILL')->detach foreach threads->list(); </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1006

</td>

<td class="new_line diff-line-num" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1024

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1024" class="line" lang="perl"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1007

</td>

<td class="new_line diff-line-num" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1025

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1025" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;">#&generate_indices(@files);  # Generate index files for blast</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1008

</td>

<td class="new_line diff-line-num" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1026

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1026" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$desc</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1297,6 +1315,8 @@ sub hmmWorker {</td>

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<td class="old_line diff-line-num" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1297

</td>

<td class="new_line diff-line-num" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1315

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1315" class="line" lang="perl">    <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1298

</td>

<td class="new_line diff-line-num" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1316

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1316" class="line" lang="perl">  <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1299

</td>

<td class="new_line diff-line-num" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1317

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1317" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FHret</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1318

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1318" class="line" lang="perl"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1319

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1319" class="line" lang="perl">  <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">exit</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1300

</td>

<td class="new_line diff-line-num" data-linenumber="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1320

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1320" class="line" lang="perl"><span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1301

</td>

<td class="new_line diff-line-num" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1321

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1321" class="line" lang="perl"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1302

</td>

<td class="new_line diff-line-num" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1322

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1322" class="line" lang="perl"></span>

</pre></td>

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<tr class="line_holder match" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1696,6 +1716,8 @@ sub workerthread {</td>

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<td class="old_line diff-line-num" data-linenumber="1696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1696

</td>

<td class="new_line diff-line-num" data-linenumber="1716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1716

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1716" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">unlink</span><span class="p">("</span><span class="si" style="color: #d14;">$temp_file</span><span class="s2" style="color: #d14;">.log</span><span class="p">");</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1697

</td>

<td class="new_line diff-line-num" data-linenumber="1717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1717

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1717" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">unlink</span><span class="p">("</span><span class="si" style="color: #d14;">$temp_file</span><span class="s2" style="color: #d14;">.tmp.matching</span><span class="p">");</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1698

</td>

<td class="new_line diff-line-num" data-linenumber="1718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1718

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1718" class="line" lang="perl"></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1719

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1719" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$last_jobs_time</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">time</span><span class="p">();</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1720

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1720" class="line" lang="perl"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1699

</td>

<td class="new_line diff-line-num" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1721

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1721" class="line" lang="perl">  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1700

</td>

<td class="new_line diff-line-num" data-linenumber="1722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1722

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1722" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$i</span><span class="p">,</span> <span class="nv" style="color: #008080;">$j</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1701

</td>

<td class="new_line diff-line-num" data-linenumber="1723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1723

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1723" class="line" lang="perl">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1704,20 +1726,20 @@ sub workerthread {</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1704

</td>

<td class="new_line diff-line-num" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1726

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1726" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># If there is nothing</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1705

</td>

<td class="new_line diff-line-num" data-linenumber="1727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1727

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1727" class="line" lang="perl">      <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$job</span><span class="p">))</span> <span class="p">{</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1706

</td>

<td class="new_line diff-line-num" data-linenumber="1728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1728

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1728" class="line" lang="perl">        <span class="c1" style="color: #998; font-style: italic;"># Check if more jobs need to be done</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1707

</td>

<td class="new_line diff-line-num old" data-linenumber="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1707" class="line" lang="perl"></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1708

</td>

<td class="new_line diff-line-num" data-linenumber="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1729

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1729" class="line" lang="perl">        <span class="p">{</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1709

</td>

<td class="new_line diff-line-num" data-linenumber="1730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1730

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1730" class="line" lang="perl">        <span class="nv" style="color: #008080;">lock</span><span class="p">(</span><span class="nv" style="color: #008080;">$jobs_done</span><span class="p">);</span>             <span class="c1" style="color: #998; font-style: italic;">#   Productive</span></span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1710

</td>

<td class="new_line diff-line-num old" data-linenumber="1731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1710" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$jobs_done</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: #008080;">$jobs_todo</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="nv" style="color: #008080;">$part</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$jobs_done</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: #008080;">$part</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">#   Productive</span></span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1711

</td>

<td class="new_line diff-line-num old" data-linenumber="1731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1711" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right deletion" style="background-color: #fac5cd;">#</span>       lock($all_jobs_submitted);            #   DEBUGGING</span></span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1712

</td>

<td class="new_line diff-line-num old" data-linenumber="1731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1712" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right deletion" style="background-color: #fac5cd;">#</span>       if ($all_jobs_submitted) {            #   DEBUGGING</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1731

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1731" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$jobs_done</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: #008080;">$jobs_todo</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="nv" style="color: #008080;">$part</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$jobs_done</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: #008080;">$part</span><span class="p">)</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">||</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff addition" style="background-color: #c7f0d2;">time</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">-</span></span><span class="nv" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">$last_jobs_time</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">></span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="mi" style="color: #099;"><span class="idiff right addition" style="background-color: #c7f0d2;">3600</span></span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">#   Productive</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1732

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1732" class="line" lang="perl"><span class="idiff left addition" style="background-color: #c7f0d2;">    </span>      <span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition" style="background-color: #c7f0d2;">#</span> lock($all_jobs_submitted);            #   DEBUGGING</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1733

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1733" class="line" lang="perl"><span class="idiff left addition" style="background-color: #c7f0d2;">    </span>      <span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition" style="background-color: #c7f0d2;">#</span> if ($all_jobs_submitted) {            #   DEBUGGING</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1713

</td>

<td class="new_line diff-line-num" data-linenumber="1734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1734

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1734" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Thread </span><span class="si" style="color: #d14;">$thread_id</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">is leaving</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1714

</td>

<td class="new_line diff-line-num old" data-linenumber="1735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1714" class="line" lang="perl">          <span class="k" style="font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">return</span></span><span class="p">;</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1735

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1735" class="line" lang="perl">          <span class="nv" style="color: #008080;"><span class="idiff left addition" style="background-color: #c7f0d2;">threads</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">-></span></span><span class="nb" style="color: #0086b3;"><span class="idiff right addition" style="background-color: #c7f0d2;">exit</span></span><span class="p">;</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1715

</td>

<td class="new_line diff-line-num" data-linenumber="1736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1736

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1736" class="line" lang="perl">        <span class="p">}}</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1716

</td>

<td class="new_line diff-line-num" data-linenumber="1737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1737

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1737" class="line" lang="perl">        <span class="c1" style="color: #998; font-style: italic;"># If so, wait</span></span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1717

</td>

<td class="new_line diff-line-num old" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1717" class="line" lang="perl">        <span class="idiff left right deletion" style="background-color: #fac5cd;">  </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Thread </span><span class="si" style="color: #d14;">$thread_id</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">is seeking work (</span><span class="si" style="color: #d14;">$jobs_done</span><span class="s2" style="color: #d14;"> / </span><span class="si" style="color: #d14;">$jobs_todo</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1738

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1738" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Thread </span><span class="si" style="color: #d14;">$thread_id</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">is seeking work (</span><span class="si" style="color: #d14;">$jobs_done</span><span class="s2" style="color: #d14;"> / </span><span class="si" style="color: #d14;">$jobs_todo</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1718

</td>

<td class="new_line diff-line-num" data-linenumber="1739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1739

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1739" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">sleep</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1719

</td>

<td class="new_line diff-line-num" data-linenumber="1740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1740

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1740" class="line" lang="perl">      <span class="p">}</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1720

</td>

<td class="new_line diff-line-num" data-linenumber="1741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1741

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1741" class="line" lang="perl">      <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1742

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1742" class="line" lang="perl">        <span class="nv" style="color: #008080;">$last_jobs_time</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">time</span><span class="p">();</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1721

</td>

<td class="new_line diff-line-num" data-linenumber="1743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1743

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1743" class="line" lang="perl">        <span class="c1" style="color: #998; font-style: italic;"># Parse job</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1722

</td>

<td class="new_line diff-line-num" data-linenumber="1744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1744

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1744" class="line" lang="perl">        <span class="p">(</span><span class="nv" style="color: #008080;">$i</span><span class="p">,</span> <span class="nv" style="color: #008080;">$j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">$job</span><span class="p">);</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1723

</td>

<td class="new_line diff-line-num" data-linenumber="1745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1745

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1745" class="line" lang="perl">        <span class="c1" style="color: #998; font-style: italic;"># Break the fetch loop</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -2274,27 +2296,34 @@ sub auto_cpus {</td>

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<td class="old_line diff-line-num" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2274

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<td class="new_line diff-line-num" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2296

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2296" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">log_Worker</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="2275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2275

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<td class="new_line diff-line-num" data-linenumber="2297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2297" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">local</span> <span class="nv" style="color: #008080;">$SIG</span><span class="p">{</span><span class="nv" style="color: #008080;">KILL</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sub </span><span class="p">{</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">exit</span> <span class="p">};</span></span>

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<td class="old_line diff-line-num" data-linenumber="2276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2276

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<td class="new_line diff-line-num" data-linenumber="2298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2298

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2298" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tid</span><span class="p">();</span></span>

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<td class="old_line diff-line-num old" data-linenumber="2277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

2277

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<td class="new_line diff-line-num old" data-linenumber="2299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2277" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">log_Worker : spawn</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="p">}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="2278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2299

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2299" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">log_Worker : </span><span class="si" style="color: #d14;"><span class="idiff left addition" style="background-color: #c7f0d2;">$tid</span></span><span class="s2" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>spawn</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="2278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2278

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<td class="new_line diff-line-num" data-linenumber="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2300

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2300" class="line" lang="perl">  <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nv" style="color: #008080;">$do_log</span><span class="p">){</span></span>

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<td class="old_line diff-line-num" data-linenumber="2279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2279

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<td class="new_line diff-line-num" data-linenumber="2301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2301

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2301" class="line" lang="perl">    <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nv" style="color: #008080;">$log_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">()){</span></span>

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<td class="old_line diff-line-num new" data-linenumber="2280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2302

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2302" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">log_Worker inside : </span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;"> active threads=</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="p">{</span> <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">is_running</span><span class="p">()</span> <span class="p">}</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">())</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> log_QUEUE=</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$log_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> step1_QUEUE=</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$step1_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> check_files_QUEUE=</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$check_files_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2280

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<td class="new_line diff-line-num" data-linenumber="2303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2303" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$log</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$log_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">dequeue</span><span class="p">();</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2281

</td>

<td class="new_line diff-line-num" data-linenumber="2304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2304

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2304" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="nv" style="color: #008080;">$log</span><span class="p">;</span> <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2282

</td>

<td class="new_line diff-line-num" data-linenumber="2305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2305

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2305" class="line" lang="perl">    <span class="p">}</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

2283

</td>

<td class="new_line diff-line-num old" data-linenumber="2306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2283" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">log_Worker : active threads=</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="p">{</span> <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">is_running</span><span class="p">()</span> <span class="p">}</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">())</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="2284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

2284

</td>

<td class="new_line diff-line-num old" data-linenumber="2306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2284" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$log_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$step1_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$check_files_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="p">{</span> <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">is_running</span><span class="p">()</span> <span class="p">}</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">())</span> <span class="o" style="font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">=</span>=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span><span class="nv" style="color: #008080;">$do_log</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">}</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2306

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2306" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">log_Worker : </span><span class="si" style="color: #d14;"><span class="idiff left addition" style="background-color: #c7f0d2;">$tid</span></span><span class="s2" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;"> </span>active threads=</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="p">{</span> <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">is_running</span><span class="p">()</span> <span class="p">}</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">())</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;"> log_QUEUE=</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="nv" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">$log_QUEUE</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">-></span></span><span class="nv" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">pending</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">"</span></span><span class="s2" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;"> step1_QUEUE=</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="nv" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">$step1_QUEUE</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">-></span></span><span class="nv" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">pending</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">"</span></span><span class="s2" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;"> check_files_QUEUE=</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="nv" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">$check_files_QUEUE</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">-></span></span><span class="nv" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">pending</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">"</span></span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="p">}</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2307

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2307" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$log_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$step1_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$check_files_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="p">{</span> <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">is_running</span><span class="p">()</span> <span class="p">}</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">())</span> <span class="o" style="font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;"><</span>=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span><span class="nv" style="color: #008080;">$do_log</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2285

</td>

<td class="new_line diff-line-num" data-linenumber="2308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2308

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2308" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">sleep</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2286

</td>

<td class="new_line diff-line-num" data-linenumber="2309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2309

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2309" class="line" lang="perl">  <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="2287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

2287

</td>

<td class="new_line diff-line-num old" data-linenumber="2310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2287" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">log_Worker : dead</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="2288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

2288

</td>

<td class="new_line diff-line-num old" data-linenumber="2310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2288" class="line" lang="perl">  <span class="k" style="font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">return</span></span><span class="p">;</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2310

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2310" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">log_Worker : </span><span class="si" style="color: #d14;"><span class="idiff left addition" style="background-color: #c7f0d2;">$tid</span></span><span class="s2" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>dead</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="p">}</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2311

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2311" class="line" lang="perl">  <span class="nv" style="color: #008080;"><span class="idiff left addition" style="background-color: #c7f0d2;">threads</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">-></span></span><span class="nb" style="color: #0086b3;"><span class="idiff right addition" style="background-color: #c7f0d2;">exit</span></span><span class="p">;</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2289

</td>

<td class="new_line diff-line-num" data-linenumber="2312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2312

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2312" class="line" lang="perl"><span class="p">}</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2290

</td>

<td class="new_line diff-line-num" data-linenumber="2313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2313

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2313" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">generate_indices_Worker</span> <span class="p">{</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

2291

</td>

<td class="new_line diff-line-num old" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2291" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">local</span> <span class="nv" style="color: #008080;">$SIG</span><span class="p">{</span><span class="nv" style="color: #008080;">KILL</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sub </span><span class="p">{</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">exit</span> <span class="p">};</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2292

</td>

<td class="new_line diff-line-num" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2314

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2314" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tid</span><span class="p">();</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2315

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2315" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">local</span> <span class="nv" style="color: #008080;">$SIG</span><span class="p">{</span><span class="nv" style="color: #008080;">KILL</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sub </span><span class="p">{</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">exit</span> <span class="p">};</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2316

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2316" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">generate_indices_Worker:</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;"> spawn</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2293

</td>

<td class="new_line diff-line-num" data-linenumber="2317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2317

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2317" class="line" lang="perl">  <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nv" style="color: #008080;">$step1_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">()){</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2318

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2318" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">generate_indices_Worker:</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;"> while</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2294

</td>

<td class="new_line diff-line-num" data-linenumber="2319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2319

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2319" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$step1_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">dequeue</span><span class="p">();</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2320

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2320" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)){</span><span class="k" style="font-weight: 600;">last</span><span class="p">;}</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2321

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2321" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">generate_indices_Worker:</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;"> working on </span><span class="si" style="color: #d14;">$file</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2295

</td>

<td class="new_line diff-line-num" data-linenumber="2322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2322

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2322" class="line" lang="perl">    <span class="nv" style="color: #008080;">&generate_indices</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">);</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2323

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2323" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">generate_indices_Worker:</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;"> ok with </span><span class="si" style="color: #d14;">$file</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2296

</td>

<td class="new_line diff-line-num" data-linenumber="2324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2324

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2324" class="line" lang="perl">  <span class="p">}</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

2297

</td>

<td class="new_line diff-line-num old" data-linenumber="2325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2297" class="line" lang="perl">  <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2325

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2325" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">generate_indices_Worker:</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;"> dead</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2326

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2326" class="line" lang="perl">  <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">exit</span><span class="p">;</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2298

</td>

<td class="new_line diff-line-num" data-linenumber="2327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2327

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2327" class="line" lang="perl"><span class="p">}</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2299

</td>

<td class="new_line diff-line-num" data-linenumber="2328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2328

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2328" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">generate_indices</span> <span class="p">{</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2300

</td>

<td class="new_line diff-line-num" data-linenumber="2329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2329

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2329" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span><span class="o" style="font-weight: 600;">=</span><span class="vg" style="color: #008080;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre></td>

</tr>

<tr class="line_holder match" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -2302,6 +2331,7 @@ sub generate_indices {</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="2302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2302

</td>

<td class="new_line diff-line-num" data-linenumber="2331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2331

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2331" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2303

</td>

<td class="new_line diff-line-num" data-linenumber="2332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2332

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2332" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2304

</td>

<td class="new_line diff-line-num" data-linenumber="2333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2333

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2333" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$msg</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="2305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2334

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2334" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">generate_indices:</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;"> start</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2305

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<td class="new_line diff-line-num" data-linenumber="2335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2335

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2335" class="line" lang="perl">  </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2306

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<td class="new_line diff-line-num" data-linenumber="2336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2336

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2336" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="nv" style="color: #008080;">$msg</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;">Generating indices</span><span class="p">";</span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$force</span><span class="p">){</span><span class="nv" style="color: #008080;">$msg</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;"> anyway (forced).</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="nv" style="color: #008080;">$msg</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2307

</td>

<td class="new_line diff-line-num" data-linenumber="2337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2337

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2337" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">rapsearch</span><span class="p">")</span> <span class="p">{</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -2330,16 +2360,20 @@ sub generate_indices {</td>

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<td class="old_line diff-line-num" data-linenumber="2330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2330

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<td class="new_line diff-line-num" data-linenumber="2360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2360

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2360" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2331

</td>

<td class="new_line diff-line-num" data-linenumber="2361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2361

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2361" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">$msg</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2332

</td>

<td class="new_line diff-line-num" data-linenumber="2362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2362

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2362" class="line" lang="perl">        <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet</span><span class="p">";</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="2333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2363

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2363" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">generate_indices:</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$cmd</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2333

</td>

<td class="new_line diff-line-num" data-linenumber="2364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2364

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2364" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 2>&1</span><span class="p">`;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2365

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2365" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">generate_indices:</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$cmd</span><span class="s2" style="color: #d14;"> DONE</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2334

</td>

<td class="new_line diff-line-num" data-linenumber="2366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2366

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2366" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">/--ignore-warnings/</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2335

</td>

<td class="new_line diff-line-num" data-linenumber="2367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2367

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2367" class="line" lang="perl">          <span class="nv" style="color: #008080;">$msg</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now retry with the '--ignore-warnings' option!</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2336

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<td class="new_line diff-line-num" data-linenumber="2368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2368

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2368" class="line" lang="perl">          <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet</span><span class="p">";</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2369

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2369" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$cmd</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2337

</td>

<td class="new_line diff-line-num" data-linenumber="2370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2370

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2370" class="line" lang="perl">          <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> --ignore-warnings 2>&1</span><span class="p">`;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2338

</td>

<td class="new_line diff-line-num" data-linenumber="2371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2371

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2371" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$makedb_ret</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The database generation failed once again, please investigate the output from above. There is probably something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- send this issue to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2339

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<td class="new_line diff-line-num" data-linenumber="2372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2372

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2372" class="line" lang="perl">        <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span><span class="nv" style="color: #008080;">$msg</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$msg</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2340

</td>

<td class="new_line diff-line-num" data-linenumber="2373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2373

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2373" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2341

</td>

<td class="new_line diff-line-num" data-linenumber="2374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2374

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2374" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2342

</td>

<td class="new_line diff-line-num" data-linenumber="2375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2375

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2375" class="line" lang="perl">          <span class="nv" style="color: #008080;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet</span><span class="p">";</span></span>

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<td class="old_line diff-line-num new" data-linenumber="2343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2376

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2376" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$cmd</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2343

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<td class="new_line diff-line-num" data-linenumber="2377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2377

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2377" class="line" lang="perl">          <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 2>&1</span><span class="p">`;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2344

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<td class="new_line diff-line-num" data-linenumber="2378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2378

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2378" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$makedb_ret</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The database generation failed once again, please investigate the output from above. There is probably something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- send this issue to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}</span></span>

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<td class="old_line diff-line-num" data-linenumber="2345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2345

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<td class="new_line diff-line-num" data-linenumber="2379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2379

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2379" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">ln -s '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">abs_path</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' 2>/dev/null</span><span class="p">");</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -2535,7 +2569,9 @@ sub generate_indices {</td>

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<td class="old_line diff-line-num" data-linenumber="2535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2535

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<td class="new_line diff-line-num" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2569

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2569" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">unlink</span><span class="p">('</span><span class="s1" style="color: #d14;">formatdb.log</span><span class="p">')</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="p">'</span><span class="s1" style="color: #d14;">formatdb.log</span><span class="p">';</span></span>

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<td class="old_line diff-line-num" data-linenumber="2536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2536

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<td class="new_line diff-line-num" data-linenumber="2570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2570

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2570" class="line" lang="perl">  <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="2537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2537

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<td class="new_line diff-line-num" data-linenumber="2571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2571

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2571" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##MARK_FOR_NEW_BLAST_ALGORITHM</span></span>

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<td class="old_line diff-line-num new" data-linenumber="2538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2572

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2572" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">generate_indices:</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;"> almost end</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2538

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<td class="new_line diff-line-num" data-linenumber="2573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2573

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2573" class="line" lang="perl">  <span class="nv" style="color: #008080;">$log_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">enqueue</span><span class="p">(</span><span class="nv" style="color: #008080;">$msg</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="2539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2574

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2574" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">generate_indices:</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;"> end</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

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<td class="old_line diff-line-num" data-linenumber="2539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2539

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<td class="new_line diff-line-num" data-linenumber="2575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2575" class="line" lang="perl">  <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="2540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2540

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<td class="new_line diff-line-num" data-linenumber="2576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2576

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2576" class="line" lang="perl"><span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2541

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<td class="new_line diff-line-num" data-linenumber="2577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2577

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2577" class="line" lang="perl"></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -2557,7 +2593,11 @@ sub blast {</td>

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<td class="old_line diff-line-num" data-linenumber="2557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2557

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<td class="new_line diff-line-num" data-linenumber="2593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2593

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2593" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$blastOptions_diamond</span><span class="o" style="font-weight: 600;">=</span><span class="p">'';</span> <span class="c1" style="color: #998; font-style: italic;">#additional option --sensitive (if gene length is larger than 40)</span></span>

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<td class="old_line diff-line-num" data-linenumber="2558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2558

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<td class="new_line diff-line-num" data-linenumber="2594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2594" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$max_genlen</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="old_line diff-line-num" data-linenumber="2559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2559

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<td class="new_line diff-line-num" data-linenumber="2595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2595

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2595" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">diamond</span><span class="p">"){</span></span>

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<td class="old_line diff-line-num old" data-linenumber="2560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

2560

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<td class="new_line diff-line-num old" data-linenumber="2596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2560" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastOptions</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">--more-sensitive</span><span class="p">")</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastOptions</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">--sensitive</span><span class="p">")</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="2561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2596

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2596" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastOptions</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">--ultra-sensitive</span><span class="p">")</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="2561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2597" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastOptions</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">--very-sensitive</span><span class="p">")</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span>  </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="2561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2598

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2598" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastOptions</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">--mid-sensitive</span><span class="p">")</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span>  </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="2561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2599

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2599" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastOptions</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">--fast</span><span class="p">")</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span>  </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="2561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2600

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2600" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastOptions</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">--more-sensitive</span><span class="p">")</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastOptions</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">--sensitive</span><span class="p">")</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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2561

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<td class="new_line diff-line-num" data-linenumber="2601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2601" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$max_gene_length_diamond</span><span class="p">{</span><span class="nv" style="color: #008080;">$a</span><span class="p">}</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">40</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$max_gene_length_diamond</span><span class="p">{</span><span class="nv" style="color: #008080;">$b</span><span class="p">}</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">40</span> <span class="p">){</span> <span class="nv" style="color: #008080;">$blastOptions_diamond</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">--sensitive</span><span class="p">"</span> <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="2562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2562

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<td class="new_line diff-line-num" data-linenumber="2602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2602" class="line" lang="perl">    <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

2563

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<td class="new_line diff-line-num" data-linenumber="2603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2603" class="line" lang="perl">  <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3024,8 +3064,10 @@ sub check_files {</td>

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<td class="old_line diff-line-num" data-linenumber="3024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3064" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Checking input files queue:</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$check_files_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">())</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

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<td class="old_line diff-line-num" data-linenumber="3025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3065" class="line" lang="perl"></span>

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<td class="old_line diff-line-num" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3066" class="line" lang="perl">  <span class="nv" style="color: #008080;">$do_log</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="old_line diff-line-num new" data-linenumber="3027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3067" class="line" lang="perl">  <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">kill</span><span class="p">('</span><span class="s1" style="color: #d14;">KILL</span><span class="p">')</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">detach</span> <span class="k" style="font-weight: 600;">foreach</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">();</span> </span>

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<td class="old_line diff-line-num" data-linenumber="3027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3027

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<td class="new_line diff-line-num" data-linenumber="3068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3068" class="line" lang="perl">  <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">create</span><span class="p">('</span><span class="s1" style="color: #d14;">log_Worker</span><span class="p">');</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="3028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

3028

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<td class="new_line diff-line-num old" data-linenumber="3069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC3028" class="line" lang="perl">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$cpus</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$debug</span> <span class="p">?</span> <span class="nv" style="color: #008080;">$cpus</span> <span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">create</span><span class="p">('</span><span class="s1" style="color: #d14;">check_files_Worker</span><span class="p">')</span> <span class="p">}</span> </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3069" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Creating </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$cpus</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$debug</span> <span class="p">?</span> <span class="nv" style="color: #008080;">$cpus</span> <span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> check_files_Worker (cpus=</span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3070" class="line" lang="perl">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">((</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$cpus</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">10</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$debug</span> <span class="p">?</span> <span class="nv" style="color: #008080;">$cpus</span> <span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">create</span><span class="p">('</span><span class="s1" style="color: #d14;">check_files_Worker</span><span class="p">')</span> <span class="p">}</span> </span>

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<td class="old_line diff-line-num" data-linenumber="3029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3029

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<td class="new_line diff-line-num" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3071

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3071" class="line" lang="perl">  <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">join</span><span class="p">()</span> <span class="k" style="font-weight: 600;">foreach</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">();</span> </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3030

</td>

<td class="new_line diff-line-num" data-linenumber="3072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3072

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3072" class="line" lang="perl"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3031

</td>

<td class="new_line diff-line-num" data-linenumber="3073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3073

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3073" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$all_only_one_entry</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3047,13 +3089,14 @@ sub check_files_Worker {</td>

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<td class="old_line diff-line-num" data-linenumber="3047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3047

</td>

<td class="new_line diff-line-num" data-linenumber="3089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3089

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3089" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%seen_files</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3048

</td>

<td class="new_line diff-line-num" data-linenumber="3090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3090

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3090" class="line" lang="perl">  <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nv" style="color: #008080;">$check_files_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">()){</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3049

</td>

<td class="new_line diff-line-num" data-linenumber="3091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3091

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3091" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$check_files_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">dequeue</span><span class="p">();</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

3092

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3092" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)){</span><span class="k" style="font-weight: 600;">last</span><span class="p">;}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3050

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<td class="new_line diff-line-num" data-linenumber="3093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3093

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3093" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$seen_files</span><span class="p">{</span><span class="nv" style="color: #008080;">abs_path</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)}){</span><span class="k" style="font-weight: 600;">next</span><span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3051

</td>

<td class="new_line diff-line-num" data-linenumber="3094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3094

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3094" class="line" lang="perl">    <span class="nv" style="color: #008080;">$seen_files</span><span class="p">{</span><span class="nv" style="color: #008080;">abs_path</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</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>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3052

</td>

<td class="new_line diff-line-num" data-linenumber="3095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3095

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3095" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">check_files_Worker:</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;"> working on </span><span class="si" style="color: #d14;">$file</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3053

</td>

<td class="new_line diff-line-num" data-linenumber="3096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3096

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3096" class="line" lang="perl">    <span class="nv" style="color: #008080;">&read_details</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3054

</td>

<td class="new_line diff-line-num" data-linenumber="3097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3097

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3097" class="line" lang="perl">  <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="3055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

3055

</td>

<td class="new_line diff-line-num old" data-linenumber="3098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC3055" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">check_files_Worker:dead</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

3056

</td>

<td class="new_line diff-line-num old" data-linenumber="3098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC3056" class="line" lang="perl">  <span class="k" style="font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">return</span></span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

3098

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3098" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">check_files_Worker:</span><span class="si" style="color: #d14;"><span class="idiff left addition" style="background-color: #c7f0d2;">$tid</span></span><span class="s2" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;"> </span>dead</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

3099

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3099" class="line" lang="perl">  <span class="nv" style="color: #008080;"><span class="idiff left addition" style="background-color: #c7f0d2;">threads</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">-></span></span><span class="nb" style="color: #0086b3;"><span class="idiff right addition" style="background-color: #c7f0d2;">exit</span></span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3057

</td>

<td class="new_line diff-line-num" data-linenumber="3100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3100

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3100" class="line" lang="perl"><span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3058

</td>

<td class="new_line diff-line-num" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3101

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3101" class="line" lang="perl"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3059

</td>

<td class="new_line diff-line-num" data-linenumber="3102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3102

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3102" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">convertUniprotAndNCBI</span> <span class="p">{</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3171,7 +3214,7 @@ sub read_details {</td>

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<td class="old_line diff-line-num" data-linenumber="3171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3171

</td>

<td class="new_line diff-line-num" data-linenumber="3214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3214

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3214" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3172

</td>

<td class="new_line diff-line-num" data-linenumber="3215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3215

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3215" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">,</span><span class="p">")</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3173

</td>

<td class="new_line diff-line-num" data-linenumber="3216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3216

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3216" class="line" lang="perl">        <span class="c1" style="color: #998; font-style: italic;"># 6.0.32 : check if gene name contains a comma -> this will cause problems with the proteinortho.tsv output (gene cluster speparator)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="3174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

3174

</td>

<td class="new_line diff-line-num old" data-linenumber="3217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC3174" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file_clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;"><span class="idiff left deletion" style="background-color: #fac5cd;">abs_path</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> </span><span class="nv" style="color: #008080;">$file</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

3217

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3217" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file_clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$file</span><span class="p">;</span></span>

</pre></td>

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3175

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<td class="new_line diff-line-num" data-linenumber="3218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3218

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3218" class="line" lang="perl">        <span class="nv" style="color: #008080;">$file_clean</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/(\.[^.]+)$/_clean$1/</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3176

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<td class="new_line diff-line-num" data-linenumber="3219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3219

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3219" class="line" lang="perl">        <span class="nv" style="color: #008080;">$found_comma_in_file</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3177

</td>

<td class="new_line diff-line-num" data-linenumber="3220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3220

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3220" class="line" lang="perl">        <span class="nv" style="color: #008080;">$msg</span><span class="o" style="font-weight: 600;">.=</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> [WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> input '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' contains a gene-name with a comma, this causes problems with the proteinortho.tsv output, I will clean the file ('</span><span class="si" style="color: #d14;">$file_clean</span><span class="s2" style="color: #d14;">') and restart the analysis !!!</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The line is:</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$curLine</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3216,7 +3259,7 @@ sub read_details {</td>

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3216

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<td class="new_line diff-line-num" data-linenumber="3259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3259

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3259" class="line" lang="perl"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3217

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<td class="new_line diff-line-num" data-linenumber="3260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3260

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3260" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$found_comma_in_file</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$from_synteny_call</span><span class="p">){</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3218

</td>

<td class="new_line diff-line-num" data-linenumber="3261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3261

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3261" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># 6.0.32 : replace the , with ; -> write output in a *_clean.* file</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="3219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

3219

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<td class="new_line diff-line-num old" data-linenumber="3262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC3219" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file_clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">abs_path</span> <span class="nv" style="color: #008080;">$file</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

3262

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3262" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file_clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;"><span class="idiff left addition" style="background-color: #c7f0d2;">$file</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">;</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition" style="background-color: #c7f0d2;">#</span>abs_path $file;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3220

</td>

<td class="new_line diff-line-num" data-linenumber="3263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3263

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3263" class="line" lang="perl">    <span class="nv" style="color: #008080;">$file_clean</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/(\.[^.]+)$/_clean$1/</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3221

</td>

<td class="new_line diff-line-num" data-linenumber="3264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3264

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3264" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: #008080;">FASTA</span><span class="p">,"</span><span class="s2" style="color: #d14;"><</span><span class="si" style="color: #d14;">$file</span><span class="p">")</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">Could not open '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">': $!</span><span class="p">");</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3222

</td>

<td class="new_line diff-line-num" data-linenumber="3265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3265

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3265" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: #008080;">FASTA_CLEAN</span><span class="p">,"</span><span class="s2" style="color: #d14;">></span><span class="si" style="color: #d14;">$file_clean</span><span class="p">")</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">Could not open '</span><span class="si" style="color: #d14;">$file_clean</span><span class="s2" style="color: #d14;">': $!</span><span class="p">");</span></span>

</pre></td>

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<br>

</li>

<li id="9fa949bc0321e9cba9ff960eb0439ff00683ae89">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/427c970d6dc7f60f2e664a405045ea9af4a8fe2e...85c9aa9ec8f6a1e761239bffa81ccefe3ba3779a#9fa949bc0321e9cba9ff960eb0439ff00683ae89" style="color: #1068bf;"><strong style="font-weight: bold;">src/po_tree.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -43,7 +43,7 @@ void builder(BOOL** matrix, Uint viecher, Uint ccs, char*** pnamen);</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC43" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">merge</span> <span class="p">(</span><span class="n" style="color: #333;">Uint</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max</span><span class="p">,</span> <span class="n" style="color: #333;">Uint</span> <span class="n" style="color: #333;">css</span><span class="p">,</span> <span class="n" style="color: #333;">Uint</span> <span class="n" style="color: #333;">viecher</span><span class="p">,</span> <span class="n" style="color: #333;">BOOL</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">away</span><span class="p">,</span> <span class="n" style="color: #333;">BOOL</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <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;">aff</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="n" style="color: #333;">pnamen</span><span class="p">);</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC44" class="line" lang="c"><span class="n" style="color: #333;">BOOL</span> <span class="nf" style="color: #900; font-weight: 600;">getmax</span><span class="p">(</span><span class="n" style="color: #333;">BOOL</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">BOOL</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">away</span><span class="p">,</span> <span class="n" style="color: #333;">Uint</span> <span class="n" style="color: #333;">viecher</span><span class="p">,</span> <span class="n" style="color: #333;">Uint</span> <span class="n" style="color: #333;">ccs</span><span class="p">,</span> <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;">aff</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="n" style="color: #333;">pnamen</span><span class="p">);</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC45" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">sim</span><span class="p">(</span><span class="n" style="color: #333;">BOOL</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">Uint</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">Uint</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">Uint</span> <span class="n" style="color: #333;">ccs</span><span class="p">);</span></span>

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<td class="new_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC46" 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="nf" style="color: #900; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">myitoa</span></span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">zahl</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">base</span><span class="p">);</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC46" 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="nf" style="color: #900; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">integer2string</span></span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">zahl</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">base</span><span class="p">);</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC47" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">get_number</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="n" style="color: #333;">word</span><span class="p">);</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC48" class="line" lang="c"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC49" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</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="n" style="color: #333;">argv</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -177,11 +177,11 @@ void merge (Uint* max, Uint ccs, Uint viecher, BOOL* away, BOOL** matrix, int**</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC177" class="line" lang="c"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC178" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* transform the number to text </span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC179" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">           the difference with their affinity is the new branch length (= distance) */</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC180" 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;">length_0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">myitoa</span></span><span class="p">(</span><span class="n" style="color: #333;">gemein_0</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">counter</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

181

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<td class="new_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC181" 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;">length_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">myitoa</span></span><span class="p">(</span><span class="n" style="color: #333;">gemein_1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">counter</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

180

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC180" 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;">length_0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">integer2string</span></span><span class="p">(</span><span class="n" style="color: #333;">gemein_0</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">counter</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

181

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC181" 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;">length_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">integer2string</span></span><span class="p">(</span><span class="n" style="color: #333;">gemein_1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">counter</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

182

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<td class="new_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

182

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC182" class="line" lang="c"></span>

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<td class="old_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

183

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<td class="new_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

183

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC183" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* transform the number of common genes (= affinity) to text */</span></span>

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<td class="old_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

184

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<td class="new_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC184" 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;">anz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">myitoa</span></span><span class="p">(</span><span class="n" style="color: #333;">counter</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

184

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC184" 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;">anz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">integer2string</span></span><span class="p">(</span><span class="n" style="color: #333;">counter</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

185

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<td class="new_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

185

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC185" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* calculate how many place is needed for the new string </span></span>

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<td class="old_line diff-line-num" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

186

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<td class="new_line diff-line-num" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

186

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC186" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">         sum of both species strings (= subtree) + new numbers + parenteses + : + \0 */</span></span>

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<td class="old_line diff-line-num" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC187" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pnamen</span><span class="p">)[</span><span class="n" style="color: #333;">max</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]])</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pnamen</span><span class="p">)[</span><span class="n" style="color: #333;">max</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]])</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">anz</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">length_0</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">length_1</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">8</span><span class="p">;</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -213,7 +213,7 @@ void merge (Uint* max, Uint ccs, Uint viecher, BOOL* away, BOOL** matrix, int**</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC213" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* free */</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

214

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<td class="new_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

214

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC214" class="line" lang="c">    <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">length_0</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

215

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<td class="new_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

215

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC215" class="line" lang="c">    <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">length_1</span><span class="p">);</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

216

</td>

<td class="new_line diff-line-num old" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC216" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* pointer gotten from <span class="idiff left right deletion" style="background-color: #fac5cd;">myitoa</span> */</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

216

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC216" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* pointer gotten from <span class="idiff left right addition" style="background-color: #c7f0d2;">integer2string</span> */</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

217

</td>

<td class="new_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

217

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC217" class="line" lang="c">    <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">anz</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

218

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<td class="new_line diff-line-num" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC218" class="line" lang="c"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

219

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<td class="new_line diff-line-num" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

219

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC219" class="line" lang="c"><span class="p">}</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -266,7 +266,7 @@ BOOL getmax(BOOL** matrix, BOOL* away, Uint viecher, Uint ccs, int** aff, char**</td>

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<td class="old_line diff-line-num" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

266

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<td class="new_line diff-line-num" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

266

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC266" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* if both entries are the same (as initiated), we are done */</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

267

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<td class="new_line diff-line-num" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC267" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bestpair</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bestpair</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

268

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<td class="new_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

268

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC268" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/* get the last branch length of the tree */</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

269

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<td class="new_line diff-line-num old" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC269" 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;">anz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">myitoa</span></span><span class="p">(</span><span class="n" style="color: #333;">get_number</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pnamen</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

269

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC269" 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;">anz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">integer2string</span></span><span class="p">(</span><span class="n" style="color: #333;">get_number</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pnamen</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

270

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<td class="new_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC270" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/* recalculate size of the tree */</span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC271" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pnamen</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">anz</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC272" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/* realloc */</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -274,7 +274,7 @@ BOOL getmax(BOOL** matrix, BOOL* away, Uint viecher, Uint ccs, int** aff, char**</td>

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<td class="new_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC274" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/* add the information about the root's branchlength */</span></span>

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<td class="old_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC275" class="line" lang="c">            <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pnamen</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcat</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pnamen</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="s" style="color: #d14;">":"</span><span class="p">);</span></span>

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<td class="new_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC276" class="line" lang="c">            <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pnamen</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcat</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pnamen</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">anz</span><span class="p">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC277" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/* free <span class="idiff left right deletion" style="background-color: #fac5cd;">myitoa</span>'s string */</span></span>

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<td class="old_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC277" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/* free <span class="idiff left right addition" style="background-color: #c7f0d2;">integer2string</span>'s string */</span></span>

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<td class="new_line diff-line-num" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC278" class="line" lang="c">            <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">anz</span><span class="p">);</span></span>

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<td class="new_line diff-line-num" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC279" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/* return finished */</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC280" class="line" lang="c">            <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -431,7 +431,7 @@ int get_number(char* word) {</td>

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<td class="new_line diff-line-num" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC431" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *  returns - char array representing number zahl to base base as text</span></span>

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<td class="new_line diff-line-num" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC432" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *            Attention: returnvalue needs to be freed separately</span></span>

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433

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC433" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<td class="old_line diff-line-num old" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

434

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<td class="new_line diff-line-num old" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC434" 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="nf" style="color: #900; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">myitoa</span></span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">zahl</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">base</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

434

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC434" 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="nf" style="color: #900; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">integer2string</span></span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">zahl</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">base</span><span class="p">)</span> <span class="p">{</span></span>

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435

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<td class="new_line diff-line-num" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

435

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC435" 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="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>

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436

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<td class="new_line diff-line-num" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

436

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC436" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">reverse</span><span class="p">[</span><span class="mi" style="color: #099;">64</span><span class="p">];</span></span>

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437

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<td class="new_line diff-line-num" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

437

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC437" class="line" lang="c"></span>

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<br>

</li>

<li id="ba368ee46e511166051985e745eaa37aea49d150">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/427c970d6dc7f60f2e664a405045ea9af4a8fe2e...85c9aa9ec8f6a1e761239bffa81ccefe3ba3779a#ba368ee46e511166051985e745eaa37aea49d150" style="color: #1068bf;"><strong style="font-weight: bold;">src/proteinortho_clustering.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -97,7 +97,7 @@ string getTime(void);</td>

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97

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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

97

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC97" class="line" lang="cpp">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">param_useLapack</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="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

98

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<td class="new_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

98

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC98" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

99

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<td class="new_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

99

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC99" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// min/max number of alg con iterations</span></span>

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<td class="old_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

100

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC100" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">critical_min_nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16777216</span><span class="p">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

100

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC100" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left addition" style="background-color: #c7f0d2;">// </span>unsigned int critical_min_nodes = 16777216;<span class="idiff right addition" style="background-color: #c7f0d2;"> // replaced</span></span></span>

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<td class="old_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

101

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<td class="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

101

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC101" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span>                   <span class="c1" style="color: #998; font-style: italic;">// below this value, results may vary</span></span>

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<td class="old_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

102

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<td class="new_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

102

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC102" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">param_max_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8192</span><span class="p">;</span>                  <span class="c1" style="color: #998; font-style: italic;">// below this value, results may vary</span></span>

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103

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC103" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">param_epsilon</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1e-8</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// analog to http://people.sc.fsu.edu/~jburkardt/c_src/power_method/power_method_prb.c</span></span>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -442,7 +442,7 @@ void printHelp() {</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC442" class="line" lang="cpp">  <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"         -coreMinSpecies int  the minimum number of species for -core ["</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">param_coreMinSpecies</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC443" class="line" lang="cpp">  <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">technical parameters:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC444" class="line" lang="cpp">  <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"         -test             various test-functions are called first [not set]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

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<td class="new_line diff-line-num old" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC445" class="line" lang="cpp">  <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"         -maxnodes int     only consider connected component with up to maxnodes nodes ["</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">param_max_nodes</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC445" class="line" lang="cpp">  <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"         -maxnodes int     only consider connected component with up to maxnodes nodes<span class="idiff left right addition" style="background-color: #c7f0d2;">. If exceeded, greedily remove the worst 10 percent of edges (by weight) until satisfied</span> ["</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">param_max_nodes</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC446" class="line" lang="cpp">  <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"         -maxweight int    only use the edge weights for connected components with maxweight nodes ["</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">param_max_nodes_weight</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC447" class="line" lang="cpp">  <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"         -epsilon float    convergence threshold ["</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">param_epsilon</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC448" class="line" lang="cpp">  <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"         -weighted bool    the spectral partition is calculated using the bitscores ["</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">param_useWeights</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre></td>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -876,6 +876,47 @@ struct compare_ConnectedComponents { //sort from large to small</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC876" class="line" lang="cpp">  <span class="p">}</span></span>

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877

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC877" class="line" lang="cpp"><span class="p">};</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

878

</td>

<td class="new_line diff-line-num" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

878

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC878" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

879

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC879" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">removeLowQualityEdges</span><span class="p">(</span> <span class="n" style="color: #333;">ConnectedComponent</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_cc</span> <span class="p">){</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

880

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC880" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

881

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC881" class="line" lang="cpp">          <span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

882

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC882" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">               * remove low quality edges</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

883

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC883" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">               * </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

884

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC884" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">               * find the range of values of this CC -> define a cut-off = cut_off=min_w+0.1*(max_w-min_w);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

885

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC885" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">               * remove all edges below that value</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

886

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC886" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">               * redo BFS and start over again for this cluster until -maxnodes are satisfied</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

887

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC887" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">               * </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

888

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC888" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">               */</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

889

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC889" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

890

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC890" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// find the lowest 10% of edge values (min+0.1*(max-min))</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

891

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC891" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">min_w</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

892

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC892" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_w</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

893

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC893" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</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;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</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 class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

894

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC894" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">from</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cur_cc</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

895

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC895" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">edges</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

896

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC896" class="line" lang="cpp">                          <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">edges</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">edge</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

897

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC897" class="line" lang="cpp">                          <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">edges</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">weight</span><span class="p">;</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

898

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC898" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">min_w</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_w</span><span class="p">){</span><span class="n" style="color: #333;">min_w</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">weight</span><span class="p">;}</span> </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

899

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC899" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">min_w</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_w</span><span class="p">){</span><span class="n" style="color: #333;">max_w</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">weight</span><span class="p">;}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

900

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC900" class="line" lang="cpp">                  <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

901

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC901" class="line" lang="cpp">          <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

902

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC902" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">cut_off</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">min_w</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.1</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">max_w</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">min_w</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

903

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC903" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">debug_level</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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"cut_off="</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">cut_off</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" min_w="</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">min_w</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" max_w="</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">max_w</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

904

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC904" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</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;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</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 class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

905

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC905" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">from</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cur_cc</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

906

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC906" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">remove_if</span><span class="p">(</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

907

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC907" class="line" lang="cpp">                          <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">edges</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

908

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC908" class="line" lang="cpp">                          <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">edges</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> </span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

909

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC909" class="line" lang="cpp">                          <span class="p">[</span><span class="n" style="color: #333;">cut_off</span><span class="p">,</span><span class="n" style="color: #333;">from</span><span class="p">](</span><span class="n" style="color: #333;">wedge</span> <span class="n" style="color: #333;">cur_el</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="kt" style="color: #458; font-weight: 600;">bool</span> </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

910

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC910" class="line" lang="cpp">                          <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

911

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC911" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">debug_level</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cur_el</span><span class="p">.</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">cut_off</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[WARNING] found bad-edge "</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cur_el</span><span class="p">.</span><span class="n" style="color: #333;">edge</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" weight="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cur_el</span><span class="p">.</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

912

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC912" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cur_el</span><span class="p">.</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">cut_off</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

913

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC913" class="line" lang="cpp">                          <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

914

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC914" class="line" lang="cpp">                  <span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

915

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC915" class="line" lang="cpp">                  <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">edges</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">].</span><span class="n" style="color: #333;">edges</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

916

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC916" class="line" lang="cpp">          <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

917

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC917" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

918

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC918" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

919

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC919" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

879

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<td class="new_line diff-line-num" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

920

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC920" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">find_CCs_givenNodes</span><span class="p">(</span><span class="n" style="color: #333;">dispatch_queue</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <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;">todo_work</span> <span class="p">){</span></span>

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<td class="old_line diff-line-num" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

880

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<td class="new_line diff-line-num" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

921

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC921" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

881

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<td class="new_line diff-line-num" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

922

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC922" class="line" lang="cpp">  <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">done</span><span class="p">;</span>    <span class="c1" style="color: #998; font-style: italic;">// Keep track on what was done (for each node)</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -901,7 +942,7 @@ void find_CCs_givenNodes(dispatch_queue *q, vector<unsigned int> todo_work ){</td>

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<td class="old_line diff-line-num" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

901

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<td class="new_line diff-line-num" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

942

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC942" class="line" lang="cpp">          <span class="n" style="color: #333;">allNodesAreDone</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

902

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<td class="new_line diff-line-num" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

943

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC943" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

903

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<td class="new_line diff-line-num" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

944

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC944" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</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;">todo_work</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</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 class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

904

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<td class="new_line diff-line-num old" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC904" class="line" lang="cpp"><span class="idiff left right deletion" style="background-color: #fac5cd;">                     </span></span>

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<td class="old_line diff-line-num new" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

945

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC945" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

905

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<td class="new_line diff-line-num" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

946

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC946" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">protein_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">todo_work</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

906

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<td class="new_line diff-line-num" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

947

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC947" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">done</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">protein_id</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">done</span><span class="p">[</span><span class="n" style="color: #333;">protein_id</span><span class="p">]</span> <span class="p">){</span><span class="k" style="font-weight: 600;">continue</span><span class="p">;}</span><span class="c1" style="color: #998; font-style: italic;">// We were here already</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

907

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<td class="new_line diff-line-num" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

948

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC948" class="line" lang="cpp"></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -915,19 +956,14 @@ void find_CCs_givenNodes(dispatch_queue *q, vector<unsigned int> todo_work ){</td>

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915

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<td class="new_line diff-line-num" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

956

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC956" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

916

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<td class="new_line diff-line-num" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

957

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC957" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">debug_level</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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"ConnectedComponent: @"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">getCCid</span><span class="p">(</span><span class="n" style="color: #333;">todo_work</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"=>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"@"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">getCCid</span><span class="p">(</span><span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">m_content_CC</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

917

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<td class="new_line diff-line-num" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

958

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC958" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

918

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<td class="new_line diff-line-num old" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC918" class="line" lang="cpp">                  <span class="c1" style="color: #998; font-style: italic;">// Skip those that are too large (try <span class="idiff left right deletion" style="background-color: #fac5cd;">critical edge </span>heuristic)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

919

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<td class="new_line diff-line-num old" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC919" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">param_max_nodes</span><span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">||</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">cur_cc</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">size</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">()</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">></span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff right deletion" style="background-color: #fac5cd;">critical_min_nodes</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

959

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC959" class="line" lang="cpp">                  <span class="c1" style="color: #998; font-style: italic;">// Skip those that are too large (try heuristic)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

960

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC960" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">param_max_nodes</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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920

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<td class="new_line diff-line-num" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

961

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC961" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

921

</td>

<td class="new_line diff-line-num old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC921" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">param_max_nodes</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

922

</td>

<td class="new_line diff-line-num old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC922" class="line" lang="cpp">                                  <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [WARNING]  Found a very large connected component that contains "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">param_max_nodes</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (maxnodes) elements. This behavior can be adjusted using -maxnodes, still you better consider a higher e-value or coverage thresholds. Now using the Critical-Heuristic: try to identify and remove critical edges."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

923

</td>

<td class="new_line diff-line-num old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC923" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">else</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

924

</td>

<td class="new_line diff-line-num old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC924" class="line" lang="cpp">                                  <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [WARNING]  Found a rather large connected component that contains "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">critical_min_nodes</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (critical_min_nodes) elements. Now using the Critical-Heuristic: try to identify and remove critical edges."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

925

</td>

<td class="new_line diff-line-num old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC925" class="line" lang="cpp">                          </span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

926

</td>

<td class="new_line diff-line-num old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC926" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">param_max_nodes</span><span class="p">){</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

927

</td>

<td class="new_line diff-line-num old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC927" class="line" lang="cpp">                                  <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [WARNING]  The very large connected component that contains "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" elements, did not have any critical edges."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

928

</td>

<td class="new_line diff-line-num old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC928" class="line" lang="cpp">                                  <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [WARNING]  Skipping this connected component. This behavior can be adjusted using -maxnodes, still you better consider a higher e-value or coverage thresholds."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

929

</td>

<td class="new_line diff-line-num old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC929" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> </span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

930

</td>

<td class="new_line diff-line-num old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC930" class="line" lang="cpp">                          <span class="p">}</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

962

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC962" class="line" lang="cpp">                          <span class="c1" style="color: #998; font-style: italic;">// reset done vector</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

963

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC963" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">for</span> <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="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;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span> <span class="n" style="color: #333;">done</span><span class="p">[</span><span class="n" style="color: #333;">cur_cc</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="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="p">}</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

964

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC964" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">debug_level</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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [WARNING]  Found a very large connected component that contains "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">param_max_nodes</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (maxnodes) elements. This behavior can be adjusted using -maxnodes. Now using a slow heuristic: try to identify and remove edges."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

965

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC965" class="line" lang="cpp">                          <span class="n" style="color: #333;">removeLowQualityEdges</span><span class="p">(</span><span class="n" style="color: #333;">cur_cc</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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

966

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC966" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

931

</td>

<td class="new_line diff-line-num" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

967

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC967" class="line" lang="cpp">                  <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

932

</td>

<td class="new_line diff-line-num" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

968

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC968" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

933

</td>

<td class="new_line diff-line-num" data-linenumber="969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

969

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC969" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">param_core</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">species_num</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1066,7 +1102,7 @@ void partition_CC(ConnectedComponent cur_cc, dispatch_queue *q, bool do_lapack,</td>

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<td class="old_line diff-line-num" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1066

</td>

<td class="new_line diff-line-num" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1102

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1102" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              * purity is imporatant if there are multiple clusters that can be split or there is no good split</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1067

</td>

<td class="new_line diff-line-num" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1103

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1103" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              * identified nodes (in purity boundary) are put back to the queue stack (=groupZero)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1068

</td>

<td class="new_line diff-line-num" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1104

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1104" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              * </span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1069

</td>

<td class="new_line diff-line-num old" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1069" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              * maximal purity = 0.1 -> get all nodes with |x_hat(v)|<0.1</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1105

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1105" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              * maximal purity = 0.1<span class="idiff left addition" style="background-color: #c7f0d2;">2</span> -> get all nodes with |x_hat(v)|<0.1<span class="idiff right addition" style="background-color: #c7f0d2;">2</span></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1070

</td>

<td class="new_line diff-line-num" data-linenumber="1106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1106

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1106" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              * identify all possible purity thresholds </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1071

</td>

<td class="new_line diff-line-num" data-linenumber="1107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1107

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1107" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              * each purity threshold is evaluated with the total sum of edge weights that are removed with this cut</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1072

</td>

<td class="new_line diff-line-num" data-linenumber="1108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1108

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1108" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              * find most optimal purity cut-off</span></span>

</pre></td>

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<tr class="line_holder match" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1090,7 +1126,7 @@ void partition_CC(ConnectedComponent cur_cc, dispatch_queue *q, bool do_lapack,</td>

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<td class="old_line diff-line-num" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1090

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<td class="new_line diff-line-num" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1126

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1126" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">debug_level</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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" initial purity=0 best_cut="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">best_cut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1091

</td>

<td class="new_line diff-line-num" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1127

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1127" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pi</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;">pi</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">pi</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1092

</td>

<td class="new_line diff-line-num" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1128

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1128" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_cc</span><span class="p">[</span><span class="n" style="color: #333;">pi</span><span class="p">];</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1093

</td>

<td class="new_line diff-line-num old" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1093" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">mapping</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">from</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">x_hat</span><span class="p">[</span> <span class="n" style="color: #333;">mapping</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">]</span> <span class="p">])</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.1</span> <span class="p">){</span><span class="k" style="font-weight: 600;">continue</span><span class="p">;}</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1129

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1129" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">mapping</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">from</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">x_hat</span><span class="p">[</span> <span class="n" style="color: #333;">mapping</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">]</span> <span class="p">])</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.1<span class="idiff left right addition" style="background-color: #c7f0d2;">2</span></span> <span class="p">){</span><span class="k" style="font-weight: 600;">continue</span><span class="p">;}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1094

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<td class="new_line diff-line-num" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1130

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1130" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">test_purity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">x_hat</span><span class="p">[</span> <span class="n" style="color: #333;">mapping</span><span class="p">[</span><span class="n" style="color: #333;">from</span><span class="p">]</span> <span class="p">]);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1095

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<td class="new_line diff-line-num" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1131

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1131" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">cut_value</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1096

</td>

<td class="new_line diff-line-num" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1132

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1132" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_nodes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre></td>

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<tr class="line_holder match" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1114,7 +1150,7 @@ void partition_CC(ConnectedComponent cur_cc, dispatch_queue *q, bool do_lapack,</td>

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<td class="old_line diff-line-num" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1114

</td>

<td class="new_line diff-line-num" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1150

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1150" class="line" lang="cpp">                 <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1115

</td>

<td class="new_line diff-line-num" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1151

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1151" class="line" lang="cpp">         <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1116

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<td class="new_line diff-line-num" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1152

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1152" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1117

</td>

<td class="new_line diff-line-num old" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1117" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">new_purity</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.1</span><span class="p">){</span><span class="n" style="color: #333;">new_purity</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;">// if there are no impure nodes -> disable</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1153

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1153" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">new_purity</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.1<span class="idiff left right addition" style="background-color: #c7f0d2;">2</span></span><span class="p">){</span><span class="n" style="color: #333;">new_purity</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;">// if there are no impure nodes -> disable</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1118

</td>

<td class="new_line diff-line-num" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1154

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1154" class="line" lang="cpp">         <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_impure_nodes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1119

</td>

<td class="new_line diff-line-num" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1155

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1155" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</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;">x_hat</span><span class="p">.</span><span class="n" style="color: #333;">size</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 class="p">{</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">x_hat</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="n" style="color: #333;">new_purity</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">num_impure_nodes</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="p">}</span> <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1120

</td>

<td class="new_line diff-line-num" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1156

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1156" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">debug_level</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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" num_impure_nodes"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">num_impure_nodes</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre></td>

</tr>

<tr class="line_holder match" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1391,19 +1427,14 @@ void find_CCs(dispatch_queue *q){</td>

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<td class="old_line diff-line-num" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1391

</td>

<td class="new_line diff-line-num" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1427

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1427" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// Do not report singles</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1392

</td>

<td class="new_line diff-line-num" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1428

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1428" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">continue</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;">// singletons are from no interest</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1393

</td>

<td class="new_line diff-line-num" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1429

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1429" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1394

</td>

<td class="new_line diff-line-num old" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1394" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// Skip those that are too large (try <span class="idiff left right deletion" style="background-color: #fac5cd;">critical edge </span>heuristic)</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1395

</td>

<td class="new_line diff-line-num old" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1395" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">param_max_nodes</span><span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">||</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">cur_cc</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">size</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">()</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">></span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff right deletion" style="background-color: #fac5cd;">critical_min_nodes</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1430

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1430" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// Skip those that are too large (try heuristic)</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1431

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1431" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">param_max_nodes</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1396

</td>

<td class="new_line diff-line-num" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1432

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1432" class="line" lang="cpp"></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1397

</td>

<td class="new_line diff-line-num old" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1397" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">param_max_nodes</span><span class="p">)</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1398

</td>

<td class="new_line diff-line-num old" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1398" class="line" lang="cpp">                                 <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [WARNING]  Found a very large connected component that contains "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">param_max_nodes</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (maxnodes) elements. This behavior can be adjusted using -maxnodes, still you better consider a higher e-value or coverage thresholds. Now using the Critical-Heuristic: try to identify and remove critical edges."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1399

</td>

<td class="new_line diff-line-num old" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1399" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">else</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1400

</td>

<td class="new_line diff-line-num old" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1400" class="line" lang="cpp">                                 <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [WARNING]  Found a rather large connected component that contains "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">critical_min_nodes</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (critical_min_nodes) elements. Now using the Critical-Heuristic: try to identify and remove critical edges."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1401

</td>

<td class="new_line diff-line-num old" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1401" class="line" lang="cpp">                         </span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1402

</td>

<td class="new_line diff-line-num old" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1402" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">param_max_nodes</span><span class="p">){</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1403

</td>

<td class="new_line diff-line-num old" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1403" class="line" lang="cpp">                                 <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [WARNING]  The very large connected component that contains "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" elements, did not have any critical edges."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1404

</td>

<td class="new_line diff-line-num old" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1404" class="line" lang="cpp">                                 <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [WARNING]  Skipping this connected component. This behavior can be adjusted using -maxnodes, still you better consider a higher e-value or coverage thresholds."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1405

</td>

<td class="new_line diff-line-num old" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1405" class="line" lang="cpp">                                 <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> </span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1406

</td>

<td class="new_line diff-line-num old" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1406" class="line" lang="cpp">                         <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1433

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1433" class="line" lang="cpp">                         <span class="c1" style="color: #998; font-style: italic;">// reset done vector</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1434

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1434" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">for</span> <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="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;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span> <span class="n" style="color: #333;">done</span><span class="p">[</span><span class="n" style="color: #333;">cur_cc</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="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1435

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1435" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">debug_level</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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [WARNING]  Found a very large connected component that contains "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">param_max_nodes</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (maxnodes) elements. This behavior can be adjusted using -maxnodes. Now using a slow heuristic: try to identify and remove edges."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1436

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1436" class="line" lang="cpp">                         <span class="n" style="color: #333;">removeLowQualityEdges</span><span class="p">(</span><span class="n" style="color: #333;">cur_cc</span><span class="p">);</span> <span class="n" style="color: #333;">protein_id</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1437

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1437" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1407

</td>

<td class="new_line diff-line-num" data-linenumber="1438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1438

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1438" class="line" lang="cpp">                 <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1408

</td>

<td class="new_line diff-line-num" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1439

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1439" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1409

</td>

<td class="new_line diff-line-num" data-linenumber="1440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1440

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1440" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">param_core</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cur_cc</span><span class="p">.</span><span class="n" style="color: #333;">species_num</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre></td>

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</table>

<br>

</li>

<li id="1486be463578edbd60b13d54cd9e0d2b9d4ecd99">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/427c970d6dc7f60f2e664a405045ea9af4a8fe2e...85c9aa9ec8f6a1e761239bffa81ccefe3ba3779a#1486be463578edbd60b13d54cd9e0d2b9d4ecd99" style="color: #1068bf;"><strong style="font-weight: bold;">src/proteinortho_summary.pl</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -238,7 +238,7 @@ my @keys=sort keys %species_matrix;</td>

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<td class="old_line diff-line-num" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

238

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<td class="new_line diff-line-num" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

238

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC238" class="line" lang="perl"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

239

</td>

<td class="new_line diff-line-num" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

239

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC239" class="line" lang="perl"><span class="nv" style="color: #008080;">$noheader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

240

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<td class="new_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC240" class="line" lang="perl"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

241

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<td class="new_line diff-line-num old" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC241" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;"><span class="idiff left deletion" style="background-color: #fac5cd;">STDERR</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> </span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

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<td class="old_line diff-line-num new" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC241" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

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<td class="old_line diff-line-num" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

242

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<td class="new_line diff-line-num" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC242" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;"># The adjacency matrix, the number of edges between 2 species</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

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<td class="old_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

243

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<td class="new_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC243" class="line" lang="perl"><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$ret</span><span class="p">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

244

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<td class="new_line diff-line-num" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC244" class="line" lang="perl"><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="p">";</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -269,7 +269,7 @@ $maxNumOfCharsInOneLine=`tput cols`;</td>

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<td class="old_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC269" class="line" lang="perl"><span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="p">);</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">/=</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC270" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">10</span><span class="p">){</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">160</span><span class="p">;}</span></span>

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<td class="old_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC271" class="line" lang="perl"></span>

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<td class="old_line diff-line-num old" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

272

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<td class="new_line diff-line-num old" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC272" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;"><span class="idiff left deletion" style="background-color: #fac5cd;">STDERR</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> </span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

272

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC272" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC273" class="line" lang="perl"><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">average number of edges</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

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<td class="old_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC274" class="line" lang="perl"><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$ret</span><span class="p">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC275" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -289,7 +289,7 @@ $maxNumOfCharsInOneLine=`tput cols`;</td>

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<td class="new_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC289" class="line" lang="perl"><span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="p">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC290" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">10</span><span class="p">){</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">160</span><span class="p">;}</span></span>

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<td class="old_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC291" class="line" lang="perl"></span>

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<td class="old_line diff-line-num old" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC292" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;"><span class="idiff left deletion" style="background-color: #fac5cd;">STDERR</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> </span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

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<td class="old_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC292" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

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<td class="old_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC293" class="line" lang="perl"><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;"># The 2-path matrix, the number of paths between 2 species of length 2</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

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<td class="old_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC294" class="line" lang="perl"><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$ret</span><span class="p">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC295" class="line" lang="perl"><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="p">";</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -320,7 +320,7 @@ $maxNumOfCharsInOneLine=`tput cols`;</td>

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<td class="old_line diff-line-num" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC320" class="line" lang="perl"><span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="p">);</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">/=</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC321" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">10</span><span class="p">){</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">160</span><span class="p">;}</span></span>

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<td class="old_line diff-line-num" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC322" class="line" lang="perl"></span>

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<td class="old_line diff-line-num old" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC323" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;"><span class="idiff left deletion" style="background-color: #fac5cd;">STDERR</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> </span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC323" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

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<td class="old_line diff-line-num" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

324

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<td class="new_line diff-line-num" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

324

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC324" class="line" lang="perl"><span class="nv" style="color: #008080;">processLine</span><span class="p">("</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">average number of 2-paths</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>

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<td class="old_line diff-line-num" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

325

</td>

<td class="new_line diff-line-num" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

325

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC325" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

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<td class="old_line diff-line-num" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

326

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<td class="new_line diff-line-num" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

326

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC326" class="line" lang="perl"> </span>

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