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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/kallisto">Debian Med / kallisto</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/commit/c28e1ce966c636a14a95247b7b9bfbf0cdb38f7f">c28e1ce9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-07T11:00:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.46.0+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/commit/82b4a2ebe6c41dbb5cc244bc20f152ee91bc8ec7">82b4a2eb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-07T11:00:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.46.0+dfsg'
Update to upstream version '0.46.0+dfsg'
with Debian dir 75162b3653733ab7d723329a1270b91bc8999ac7</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/commit/af4e7a0b9ac7328cadc2ad0f44b78b78235c1b5f">af4e7a0b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-07T11:00:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/commit/594048564901816af3622feffec2f8fd01ed8e3c">59404856</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-07T11:00:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/commit/1826e5ff1d9112e1ea2d0170726b8dc4b42c7411">1826e5ff</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-07T11:00:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/commit/8cd6d157945be4e834617827620010270a23d848">8cd6d157</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-07T11:03:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#72660a233293b57492d69a1aca05cd0bcc23bafd">
src/BUSData.h
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<li class="file-stats">
<a href="#742351309009b70e28c04c50b75d5287975926bb">
src/common.h
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<li class="file-stats">
<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">
src/main.cpp
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kallisto/compare/d08a75bc8a878b650f6f9d05038f20a2a8b1c800...8cd6d157945be4e834617827620010270a23d848#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kallisto (0.46.0+dfsg-1) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 07 Aug 2019 13:01:05 +0200</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">kallisto (0.45.1+dfsg-1) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Initial release (Closes: #925417)</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/kallisto/compare/d08a75bc8a878b650f6f9d05038f20a2a8b1c800...8cd6d157945be4e834617827620010270a23d848#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">12</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/kallisto/compare/d08a75bc8a878b650f6f9d05038f20a2a8b1c800...8cd6d157945be4e834617827620010270a23d848#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 12~</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libhdf5-dev,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libhts-dev</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3</span>.0</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4</span>.0</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/kallisto</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/kallisto.git</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://pachterlab.github.io/kallisto</span>
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<a href="https://salsa.debian.org/med-team/kallisto/compare/d08a75bc8a878b650f6f9d05038f20a2a8b1c800...8cd6d157945be4e834617827620010270a23d848#72660a233293b57492d69a1aca05cd0bcc23bafd"><strong>src/BUSData.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,6 +18,11 @@ struct BUSHeader {</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">text</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BUSTranscript</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">transcripts</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">ecs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">version</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">bclen</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">umilen</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"> <span class="n" style="color: #333;">BUSHeader</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">version</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">bclen</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">umilen</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">BUSData</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,8 +31,8 @@ struct BUSData {</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ec</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">flags</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"> <span class="n" style="color: #333;">BUSData</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">barcode</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">UMI</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">ec</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 class="n" style="color: #333;">count</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">flags</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pad</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">BUSData</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">barcode</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">UMI</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">ec</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 class="n" style="color: #333;">count</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">flags</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pad</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)</span></span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="nf" style="color: #900; font-weight: 600;">stringToBinary</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kallisto/compare/d08a75bc8a878b650f6f9d05038f20a2a8b1c800...8cd6d157945be4e834617827620010270a23d848#742351309009b70e28c04c50b75d5287975926bb"><strong>src/common.h</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef KALLISTO_COMMON_H</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KALLISTO_COMMON_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KALLISTO_VERSION "0.4<span class="idiff left right">5.1</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KALLISTO_VERSION "0.4<span class="idiff left right">6.0</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<a href="https://salsa.debian.org/med-team/kallisto/compare/d08a75bc8a878b650f6f9d05038f20a2a8b1c800...8cd6d157945be4e834617827620010270a23d848#b958235ee8db37bcaceda04b6d55553b450c2db4"><strong>src/main.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -600,6 +600,106 @@ void ParseOptionsBus(int argc, char **argv, ProgramOptions& opt) {</td>
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">ParseTechnology</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">techstr</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">files</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">errorList</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bcValues</span><span class="p">)</span> <span class="p">{</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lastIndex</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;">//the last place in the string a colon and punctuation was found</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">currValue</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;">//tells us the index of the three sequences needed barcode, umi, sequence</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="cpp"> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">numbers</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//stores the numbers in a pairs</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">punctuationCompare</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">','</span><span class="p">;</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">colonCompare</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">':'</span><span class="p">;</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">colon</span><span class="p">;</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">duplicate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">stringVal</span><span class="p">;</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp"></span>
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614
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<pre style="margin: 0;">+<span id="LC614" 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;">1</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;">techstr</span><span class="p">.</span><span class="n" style="color: #333;">length</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>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp"> <span class="n" style="color: #333;">colon</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">techstr</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;">colonCompare</span><span class="p">)</span> <span class="p">{</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp"> <span class="n" style="color: #333;">colon</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"> <span class="p">}</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">techstr</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;">punctuationCompare</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">colon</span><span class="p">)</span> <span class="p">{</span></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"> <span class="n" style="color: #333;">stringVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">techstr</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">lastIndex</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;">lastIndex</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">stringVal</span><span class="p">);</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="n" style="color: #333;">numbers</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">);</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numbers</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
626
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<pre style="margin: 0;">+<span id="LC626" 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;">files</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" 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;">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;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</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 class="p">{</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span> <span class="p">{</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"> <span class="n" style="color: #333;">duplicate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp"> <span class="p">}</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"> <span class="p">}</span></span>
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633
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<pre style="margin: 0;">+<span id="LC633" 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;">duplicate</span><span class="p">)</span> <span class="p">{</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="cpp"> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">);</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp"> <span class="n" style="color: #333;">duplicate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp"> <span class="p">}</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="cpp"> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">);</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp"> <span class="p">}</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp"> <span class="p">}</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp"> <span class="n" style="color: #333;">lastIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">invalid_argument</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ia</span><span class="p">)</span> <span class="p">{</span></span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="cpp"> <span class="n" style="color: #333;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Invalid argument"</span><span class="p">);</span></span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="cpp"> <span class="p">}</span></span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="cpp"></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">colon</span><span class="p">)</span> <span class="p">{</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numbers</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;">3</span><span class="p">)</span> <span class="p">{</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="cpp"> <span class="n" style="color: #333;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Wrong number of pairs provided"</span><span class="p">);</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="cpp"> <span class="p">}</span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="cpp"> <span class="p">}</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp"> <span class="p">}</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numbers</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;">3</span><span class="p">)</span> <span class="p">{</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">currValue</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>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"> <span class="n" style="color: #333;">bcValues</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="n" style="color: #333;">numbers</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">numbers</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">numbers</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]));</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="cpp"> <span class="n" style="color: #333;">values</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="n" style="color: #333;">numbers</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">numbers</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">numbers</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]));</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="cpp"> <span class="p">}</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="cpp"> <span class="n" style="color: #333;">numbers</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="cpp"> <span class="p">}</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">colon</span><span class="p">)</span> <span class="p">{</span></span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="cpp"> <span class="n" style="color: #333;">currValue</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp"> <span class="p">}</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="cpp"></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp"> <span class="n" style="color: #333;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: parsing technology string </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">techstr</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="cpp"></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" 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;">k</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="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">files</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;">1</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</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;">files</span><span class="p">[</span><span class="n" style="color: #333;">k</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>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp"> <span class="n" style="color: #333;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: files aren't correctly referenced"</span><span class="p">);</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="cpp"> <span class="p">}</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"> <span class="p">}</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="cpp"></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp"> <span class="n" style="color: #333;">stringVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">techstr</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">lastIndex</span><span class="p">,</span> <span class="n" style="color: #333;">techstr</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">lastIndex</span><span class="p">);</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numbers</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>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">stringVal</span><span class="p">);</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"> <span class="n" style="color: #333;">numbers</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">);</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"> <span class="n" style="color: #333;">values</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="n" style="color: #333;">numbers</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">numbers</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">numbers</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]));</span></span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"> <span class="n" style="color: #333;">numbers</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span> </span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">invalid_argument</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ia</span><span class="p">)</span> <span class="p">{</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> <span class="n" style="color: #333;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Invalid argument"</span><span class="p">);</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="cpp"> <span class="p">}</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"> <span class="n" style="color: #333;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Wrong number of pairs provided"</span><span class="p">);</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"> <span class="p">}</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">currValue</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="cpp"> <span class="n" style="color: #333;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Wrong number of substrings provided"</span><span class="p">);</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp"></span>
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703
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="cpp"></span>
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604
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704
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ParseOptionsH5Dump</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="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">opt</span><span class="p">)</span> <span class="p">{</span></span>
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605
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705
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">peek_flag</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="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -762,8 +862,25 @@ bool CheckOptionsBus(ProgramOptions& opt) {</td>
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762
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862
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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863
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">));</span></span>
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764
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864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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765
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<pre style="margin: 0;">-<span id="LC765" 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;">"Unknown technology: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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766
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="cpp"> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">files</span><span class="p">;</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bcValues</span><span class="p">;</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">errorList</span><span class="p">;</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">invalid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ParseTechnology</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">files</span><span class="p">,</span> <span class="n" style="color: #333;">errorList</span><span class="p">,</span> <span class="n" style="color: #333;">bcValues</span><span class="p">);</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" 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;">invalid</span><span class="p">)</span> <span class="p">{</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> </span>
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872
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<pre style="margin: 0;">+<span id="LC872" 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;">bcValues</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>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">bcValues</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="cpp"> <span class="p">}</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" 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;">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;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">size</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 class="p">{</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">errorList</span><span class="p">[</span><span class="n" style="color: #333;">j</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>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="cpp"> <span class="p">}</span></span>
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881
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<pre style="margin: 0;">+<span id="LC881" 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;">"Unable to create technology: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="cpp"> <span class="p">}</span></span>
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767
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884
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="cpp"> <span class="p">}</span></span>
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768
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885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="cpp"> <span class="p">}</span></span>
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769
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886
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="cpp"></span>
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