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<h3>
Tomasz Buchert pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mothur">Debian Med / mothur</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mothur/-/commit/ddca3f106fbbf76262cc87299af250641abd8e93">ddca3f10</a></strong>
<div>
<span>by Tomasz Buchert</span>
<i>at 2020-09-04T09:29:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.44.3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mothur/-/commit/79abd0c5b1995dd2ce822c77e80d7fa6b18f8456">79abd0c5</a></strong>
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<span>by Tomasz Buchert</span>
<i>at 2020-09-04T10:38:38+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'upstream' into new-upstream
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#8b67dc09b93b38e95da2a54036fa1db5b207cc5b">
Mothur.xcodeproj/project.pbxproj
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<li class="file-stats">
<a href="#f179565b0222d729ba14d4ccb444f9b1c1e38dc2">
source/commands/makecontigscommand.cpp
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</li>
<li class="file-stats">
<a href="#307eb22b393b6e24c84a1f5f781bb1de30adfcfd">
source/commands/trimseqscommand.cpp
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<li class="file-stats">
<a href="#4356bb76a146ce04fb34b84f985b7c6d5e5c2c71">
source/commands/trimseqscommand.h
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</li>
</ul>
<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/mothur/-/compare/3fb847522be597c27070057314421a173fc780f8...79abd0c5b1995dd2ce822c77e80d7fa6b18f8456#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="37" 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">@@ -37,7 +37,7 @@ GSL_LIBRARY_DIR ?= "\"Enter_your_GSL_library_path_here\""</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"><span class="nv" style="color: #008080;">GSL_INCLUDE_DIR</span> <span class="o" style="font-weight: 600;">?=</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">Enter_your_GSL_include_path_here</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new_line" data-linenumber="38" 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="LC38" class="line" lang="make"><span class="nv" style="color: #008080;">MOTHUR_FILES</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">Enter_your_default_path_here</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new_line" data-linenumber="39" 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="LC39" class="line" lang="make"><span class="nv" style="color: #008080;">MOTHUR_TOOLS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">Enter_your_mothur_tools_path_here</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">1.44.<span class="idiff left right">2</span></span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">1.44.<span class="idiff left right">3</span></span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Set a static logfile name</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="124" 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="124" 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">@@ -124,7 +124,7 @@ mothur : $(OBJECTS) uchime</td>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CXX)</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(TARGET_ARCH)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$(OBJECTS)</span> <span class="nv" style="color: #008080;">$(LIBS)</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="make"><span class="nl">uchime </span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd source</span>/uchime_src <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">CXX</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CXX)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">./make clean </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> ./</span>make <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">mv </span>uchime ../../ <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd source</span>/uchime_src <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">CXX</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CXX)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left">make clean </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span>make <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">mv </span>uchime ../../ <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC129" 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;">mothur</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/mothur/-/compare/3fb847522be597c27070057314421a173fc780f8...79abd0c5b1995dd2ce822c77e80d7fa6b18f8456#8b67dc09b93b38e95da2a54036fa1db5b207cc5b"><strong>Mothur.xcodeproj/project.pbxproj</strong></a>
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<pre style="margin: 0;"> <span id="LC3944" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="l">GCC_OPTIMIZATION_LEVEL</span><span class="w" style="color: #bbb;"> </span><span class="p">=</span><span class="w" style="color: #bbb;"> </span><span class="l">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC3945" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="l">GCC_PREPROCESSOR_DEFINITIONS</span><span class="w" style="color: #bbb;"> </span><span class="p">=</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC3946" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\""</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC3947" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"VERSION=\"\\\"1.44.<span class="idiff left right">0</span>\\\"\""</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC3947" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"VERSION=\"\\\"1.44.<span class="idiff left right">3</span>\\\"\""</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC3948" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"LOGFILE_NAME=\"\\\"silent\\\"\""</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC3949" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"MOTHUR_TOOLS=\"\\\"/Users/sarahwestcott/desktop/mothur/TARGET_BUILD_DIRTARGET_BUILD_DIR/tools/\\\"\""</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC3950" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC3995" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="l">GCC_OPTIMIZATION_LEVEL</span><span class="w" style="color: #bbb;"> </span><span class="p">=</span><span class="w" style="color: #bbb;"> </span><span class="l">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC3996" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="l">GCC_PREPROCESSOR_DEFINITIONS</span><span class="w" style="color: #bbb;"> </span><span class="p">=</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC3997" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\""</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC3999" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"LOGFILE_NAME=\"\\\"./mothur.logfile\\\"\""</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC4000" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"MOTHUR_TOOLS=\"\\\"/Users/sarahwestcott/desktop/mothur/TARGET_BUILD_DIRTARGET_BUILD_DIR/tools/\\\"\""</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC4001" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC4061" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="l">GCC_OPTIMIZATION_LEVEL</span><span class="w" style="color: #bbb;"> </span><span class="p">=</span><span class="w" style="color: #bbb;"> </span><span class="l">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4062" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="l">GCC_PREPROCESSOR_DEFINITIONS</span><span class="w" style="color: #bbb;"> </span><span class="p">=</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC4063" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\""</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC4067" class="line" lang="plist"><span class="w" style="color: #bbb;"> </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">@@ -4146,7 +4146,7 @@</td>
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<pre style="margin: 0;"> <span id="LC4146" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="l">GCC_NO_COMMON_BLOCKS</span><span class="w" style="color: #bbb;"> </span><span class="p">=</span><span class="w" style="color: #bbb;"> </span><span class="l">YES</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4147" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="l">GCC_OPTIMIZATION_LEVEL</span><span class="w" style="color: #bbb;"> </span><span class="p">=</span><span class="w" style="color: #bbb;"> </span><span class="l">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4148" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="l">GCC_PREPROCESSOR_DEFINITIONS</span><span class="w" style="color: #bbb;"> </span><span class="p">=</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC4149" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"VERSION=\"\\\"1.44.<span class="idiff left right">0</span>\\\"\""</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/mothur/-/compare/3fb847522be597c27070057314421a173fc780f8...79abd0c5b1995dd2ce822c77e80d7fa6b18f8456#f179565b0222d729ba14d4ccb444f9b1c1e38dc2"><strong>source/commands/makecontigscommand.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">@@ -34,7 +34,9 @@ double convertProbToQ(double prob){</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">convertQToProb</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Q</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">Q</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">10</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">Q</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">10</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">isinf</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span> <span class="p">{</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">MothurOut</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m</span><span class="p">;</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MothurOut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getInstance</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">@@ -758,7 +760,7 @@ struct contigsData {</td>
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758
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="cpp"> <span class="n" style="color: #333;">kmerSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">km</span><span class="p">;</span></span>
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759
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="cpp"> <span class="n" style="color: #333;">align</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">al</span><span class="p">;</span></span>
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760
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="cpp"> <span class="n" style="color: #333;">deltaq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delt</span><span class="p">;</span></span>
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761
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">maxee</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxe</span><span class="p">;</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">maxee</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxe</span><span class="p">;</span></span>
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="cpp"> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">form</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="cpp"> <span class="n" style="color: #333;">trimOverlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to</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="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">@@ -1610,8 +1612,8 @@ vector<int> trimBarCodesAndPrimers(Sequence& fSeq, Sequence& rSeq, QualityScores</td>
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1610
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1612
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<pre style="margin: 0;"> <span id="LC1612" class="line" lang="cpp"> <span class="n" style="color: #333;">savedFSeq</span><span class="p">.</span><span class="n" style="color: #333;">reverseComplement</span><span class="p">();</span></span>
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1613
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<pre style="margin: 0;"> <span id="LC1613" class="line" lang="cpp"> <span class="n" style="color: #333;">savedRSeq</span><span class="p">.</span><span class="n" style="color: #333;">reverseComplement</span><span class="p">();</span></span>
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1614
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<pre style="margin: 0;"> <span id="LC1614" class="line" lang="cpp"> <span class="p">}</span></span>
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1613
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<pre style="margin: 0;">-<span id="LC1613" class="line" lang="cpp"> <span class="n" style="color: #333;">fSeq</span><span class="p">.</span><span class="n" style="color: #333;">setAligned</span><span class="p">(</span><span class="n" style="color: #333;">savedFSeq</span><span class="p">.</span><span class="n" style="color: #333;">get<span class="idiff left right">A</span>ligned</span><span class="p">());</span></span>
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1614
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<pre style="margin: 0;">-<span id="LC1614" class="line" lang="cpp"> <span class="n" style="color: #333;">rSeq</span><span class="p">.</span><span class="n" style="color: #333;">setAligned</span><span class="p">(</span><span class="n" style="color: #333;">savedRSeq</span><span class="p">.</span><span class="n" style="color: #333;">get<span class="idiff left right">A</span>ligned</span><span class="p">());</span></span>
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1615
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<pre style="margin: 0;">+<span id="LC1615" class="line" lang="cpp"> <span class="n" style="color: #333;">fSeq</span><span class="p">.</span><span class="n" style="color: #333;">setAligned</span><span class="p">(</span><span class="n" style="color: #333;">savedFSeq</span><span class="p">.</span><span class="n" style="color: #333;">get<span class="idiff left right">Una</span>ligned</span><span class="p">());</span></span>
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1616
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<pre style="margin: 0;">+<span id="LC1616" class="line" lang="cpp"> <span class="n" style="color: #333;">rSeq</span><span class="p">.</span><span class="n" style="color: #333;">setAligned</span><span class="p">(</span><span class="n" style="color: #333;">savedRSeq</span><span class="p">.</span><span class="n" style="color: #333;">get<span class="idiff left right">Una</span>ligned</span><span class="p">());</span></span>
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1617
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<pre style="margin: 0;"> <span id="LC1617" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">hasQuality</span><span class="p">){</span></span>
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1616
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1618
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<pre style="margin: 0;"> <span id="LC1618" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//checkOrient trimOligos - reoriented and reversed</span></span>
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<pre style="margin: 0;"> <span id="LC1619" class="line" lang="cpp"> <span class="n" style="color: #333;">savedFQual</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flipQScores</span><span class="p">();</span></span>
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<a href="https://salsa.debian.org/med-team/mothur/-/compare/3fb847522be597c27070057314421a173fc780f8...79abd0c5b1995dd2ce822c77e80d7fa6b18f8456#307eb22b393b6e24c84a1f5f781bb1de30adfcfd"><strong>source/commands/trimseqscommand.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">@@ -13,40 +13,40 @@</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//**********************************************************************************************************************</span></span>
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<pre style="margin: 0;">-<span id="LC16" 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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TrimSeqsCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setParameters</span><span class="p">(){</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pfasta</span><span class="p">(</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"InputTypes"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pfasta</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">poligos</span><span class="p">(</span><span class="s" style="color: #d14;">"oligos"</span><span class="p">,</span> <span class="s" style="color: #d14;">"InputTypes"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span><span class="s" style="color: #d14;">"group"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">poligos</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqfile</span><span class="p">(</span><span class="s" style="color: #d14;">"qfile"</span><span class="p">,</span> <span class="s" style="color: #d14;">"InputTypes"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span><span class="s" style="color: #d14;">"qfile"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqfile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pname</span><span class="p">(</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"InputTypes"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"namecount"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pname</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC16" 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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TrimSeqsCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setParameters</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pfasta</span><span class="p">(</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"InputTypes"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pfasta</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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="LC19" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">poligos</span><span class="p">(</span><span class="s" style="color: #d14;">"oligos"</span><span class="p">,</span> <span class="s" style="color: #d14;">"InputTypes"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span><span class="s" style="color: #d14;">"group"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">poligos</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqfile</span><span class="p">(</span><span class="s" style="color: #d14;">"qfile"</span><span class="p">,</span> <span class="s" style="color: #d14;">"InputTypes"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span><span class="s" style="color: #d14;">"qfile"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqfile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pname</span><span class="p">(</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"InputTypes"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"namecount"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pname</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pcount</span><span class="p">(</span><span class="s" style="color: #d14;">"count"</span><span class="p">,</span> <span class="s" style="color: #d14;">"InputTypes"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"namecount"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">,</span><span class="s" style="color: #d14;">"count"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pcount</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pflip</span><span class="p">(</span><span class="s" style="color: #d14;">"flip"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Boolean"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"F"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pflip</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pflip</span><span class="p">(</span><span class="s" style="color: #d14;">"flip"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Boolean"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"F"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pflip</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">preorient</span><span class="p">(</span><span class="s" style="color: #d14;">"checkorient"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Boolean"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"F"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">preorient</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pmaxambig</span><span class="p">(</span><span class="s" style="color: #d14;">"maxambig"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"-1"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pmaxambig</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pmaxhomop</span><span class="p">(</span><span class="s" style="color: #d14;">"maxhomop"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pmaxhomop</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pminlength</span><span class="p">(</span><span class="s" style="color: #d14;">"minlength"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pminlength</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pmaxlength</span><span class="p">(</span><span class="s" style="color: #d14;">"maxlength"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pmaxlength</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">ppdiffs</span><span class="p">(</span><span class="s" style="color: #d14;">"pdiffs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ppdiffs</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pbdiffs</span><span class="p">(</span><span class="s" style="color: #d14;">"bdiffs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pbdiffs</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pmaxambig</span><span class="p">(</span><span class="s" style="color: #d14;">"maxambig"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"-1"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pmaxambig</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="26" 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="LC26" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pmaxhomop</span><span class="p">(</span><span class="s" style="color: #d14;">"maxhomop"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pmaxhomop</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="27" 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="LC27" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pminlength</span><span class="p">(</span><span class="s" style="color: #d14;">"minlength"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pminlength</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="28" 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="LC28" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pmaxlength</span><span class="p">(</span><span class="s" style="color: #d14;">"maxlength"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pmaxlength</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="29" 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="LC29" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">ppdiffs</span><span class="p">(</span><span class="s" style="color: #d14;">"pdiffs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ppdiffs</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pbdiffs</span><span class="p">(</span><span class="s" style="color: #d14;">"bdiffs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pbdiffs</span><span class="p">);</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pldiffs</span><span class="p">(</span><span class="s" style="color: #d14;">"ldiffs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pldiffs</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">psdiffs</span><span class="p">(</span><span class="s" style="color: #d14;">"sdiffs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">psdiffs</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">psdiffs</span><span class="p">(</span><span class="s" style="color: #d14;">"sdiffs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">psdiffs</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">ptdiffs</span><span class="p">(</span><span class="s" style="color: #d14;">"tdiffs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ptdiffs</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pprocessors</span><span class="p">(</span><span class="s" style="color: #d14;">"processors"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pprocessors</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pallfiles</span><span class="p">(</span><span class="s" style="color: #d14;">"allfiles"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Boolean"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"F"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pallfiles</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pkeepforward</span><span class="p">(</span><span class="s" style="color: #d14;">"keepforward"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Boolean"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"F"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pkeepforward</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pprocessors</span><span class="p">(</span><span class="s" style="color: #d14;">"processors"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pprocessors</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pallfiles</span><span class="p">(</span><span class="s" style="color: #d14;">"allfiles"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Boolean"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"F"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pallfiles</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pkeepforward</span><span class="p">(</span><span class="s" style="color: #d14;">"keepforward"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Boolean"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"F"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pkeepforward</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">plogtransform</span><span class="p">(</span><span class="s" style="color: #d14;">"logtransform"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Boolean"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"F"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">plogtransform</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqtrim</span><span class="p">(</span><span class="s" style="color: #d14;">"qtrim"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Boolean"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqtrim</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqthreshold</span><span class="p">(</span><span class="s" style="color: #d14;">"qthreshold"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqthreshold</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqaverage</span><span class="p">(</span><span class="s" style="color: #d14;">"qaverage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqaverage</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">prollaverage</span><span class="p">(</span><span class="s" style="color: #d14;">"rollaverage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">prollaverage</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqwindowaverage</span><span class="p">(</span><span class="s" style="color: #d14;">"qwindowaverage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqwindowaverage</span><span class="p">);</span></span>
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<td class="diff-line-num new_line old" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqstepsize</span><span class="p">(</span><span class="s" style="color: #d14;">"qstepsize"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqstepsize</span><span class="p">);</span></span>
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<td class="diff-line-num new_line old" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqwindowsize</span><span class="p">(</span><span class="s" style="color: #d14;">"qwindowsize"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"50"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqwindowsize</span><span class="p">);</span></span>
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<td class="diff-line-num new_line old" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pkeepfirst</span><span class="p">(</span><span class="s" style="color: #d14;">"keepfirst"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pkeepfirst</span><span class="p">);</span></span>
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<td class="diff-line-num new_line old" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">premovelast</span><span class="p">(</span><span class="s" style="color: #d14;">"removelast"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">premovelast</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pseed</span><span class="p">(</span><span class="s" style="color: #d14;">"seed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pseed</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqtrim</span><span class="p">(</span><span class="s" style="color: #d14;">"qtrim"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Boolean"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqtrim</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqthreshold</span><span class="p">(</span><span class="s" style="color: #d14;">"qthreshold"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqthreshold</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqaverage</span><span class="p">(</span><span class="s" style="color: #d14;">"qaverage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqaverage</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">prollaverage</span><span class="p">(</span><span class="s" style="color: #d14;">"rollaverage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">prollaverage</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="42" 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="LC42" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqwindowaverage</span><span class="p">(</span><span class="s" style="color: #d14;">"qwindowaverage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqwindowaverage</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqstepsize</span><span class="p">(</span><span class="s" style="color: #d14;">"qstepsize"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqstepsize</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="44" 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="LC44" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pqwindowsize</span><span class="p">(</span><span class="s" style="color: #d14;">"qwindowsize"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"50"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pqwindowsize</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="45" 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="LC45" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pkeepfirst</span><span class="p">(</span><span class="s" style="color: #d14;">"keepfirst"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pkeepfirst</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" 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="LC46" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">premovelast</span><span class="p">(</span><span class="s" style="color: #d14;">"removelast"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">premovelast</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="47" 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="LC47" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pseed</span><span class="p">(</span><span class="s" style="color: #d14;">"seed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pseed</span><span class="p">);</span></span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">pinputdir</span><span class="p">(</span><span class="s" style="color: #d14;">"inputdir"</span><span class="p">,</span> <span class="s" style="color: #d14;">"String"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pinputdir</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">poutputdir</span><span class="p">(</span><span class="s" style="color: #d14;">"outputdir"</span><span class="p">,</span> <span class="s" style="color: #d14;">"String"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">poutputdir</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">CommandParameter</span> <span class="n" style="color: #333;">poutputdir</span><span class="p">(</span><span class="s" style="color: #d14;">"outputdir"</span><span class="p">,</span> <span class="s" style="color: #d14;">"String"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">poutputdir</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> </span>
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51
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<pre style="margin: 0;"> <span id="LC51" 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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tempOutNames</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempOutNames</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" 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="56" 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">@@ -56,70 +56,70 @@ vector<string> TrimSeqsCommand::setParameters(){</td>
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"count"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempOutNames</span><span class="p">;</span></span>
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57
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> </span>
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58
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="n" style="color: #333;">calledHelp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="n" style="color: #333;">comboStarts</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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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">vector</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;">myArray</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">myArray</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">myArray</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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65
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<td class="diff-line-num new_line old" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"setParameters"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">vector</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;">myArray</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">myArray</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">myArray</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"setParameters"</span><span class="p">);</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="p">}</span></span>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//**********************************************************************************************************************</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">TrimSeqsCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getHelpString</span><span class="p">(){</span><span class="idiff left right"> </span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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73
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<td class="diff-line-num new_line old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The trim.seqs command reads a fastaFile and creates 2 new fasta files, .trim.fasta and scrap.fasta, as well as group files if you provide and oligos file.</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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74
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<td class="diff-line-num new_line old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The .trim.fasta contains sequences that meet your requirements, and the .scrap.fasta contains those which don't.</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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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The trim.seqs command parameters are fasta, name, count, flip, checkorient, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast, logtransform and allfiles.</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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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The fasta parameter is required.</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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77
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<td class="diff-line-num new_line old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.</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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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">TrimSeqsCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getHelpString</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The trim.seqs command reads a fastaFile and creates 2 new fasta files, .trim.fasta and scrap.fasta, as well as group files if you provide and oligos file.</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="diff-line-num new new_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The .trim.fasta contains sequences that meet your requirements, and the .scrap.fasta contains those which don't.</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="diff-line-num new new_line" data-linenumber="75" 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">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The trim.seqs command parameters are fasta, name, count, flip, checkorient, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast, logtransform and allfiles.</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="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The fasta parameter is required.</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="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.</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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78
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<td class="diff-line-num new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The checkorient parameter will check the reverse compliment of the sequence if the barcodes and primers cannot be found in the forward. The default is false.</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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79
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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The oligos parameter allows you to provide an oligos file.</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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80
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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The name parameter allows you to provide a names file with your fasta file.</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="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The oligos parameter allows you to provide an oligos file.</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="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The name parameter allows you to provide a names file with your fasta file.</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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81
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<td class="diff-line-num new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The count parameter allows you to provide a count file with your fasta file.</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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82
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The maxambig parameter allows you to set the maximum number of ambiguous bases allowed. The default is -1.</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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83
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The maxhomop parameter allows you to set a maximum homopolymer length. </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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84
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The minlength parameter allows you to set and minimum sequence length. </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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85
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The maxlength parameter allows you to set and maximum sequence length. </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="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
86
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.</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="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
87
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.</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="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
88
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.</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="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The maxambig parameter allows you to set the maximum number of ambiguous bases allowed. The default is -1.</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="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The maxhomop parameter allows you to set a maximum homopolymer length. </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="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The minlength parameter allows you to set and minimum sequence length. </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="diff-line-num new new_line" data-linenumber="85" 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">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The maxlength parameter allows you to set and maximum sequence length. </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="diff-line-num new new_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.</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="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.</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="diff-line-num new new_line" data-linenumber="88" 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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.</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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89
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<td class="diff-line-num new_line" data-linenumber="89" 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">
89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.</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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90
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<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.</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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91
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<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qfile parameter allows you to provide a quality file.</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="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
92
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<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qthreshold parameter allows you to set a minimum quality score allowed. </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="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
93
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<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qaverage parameter allows you to set a minimum average quality score allowed. </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="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
94
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<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qwindowsize parameter allows you to set a number of bases in a window. Default=50.</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="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
95
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<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qwindowaverage parameter allows you to set a minimum average quality score allowed over a window. </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="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
96
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<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The rollaverage parameter allows you to set a minimum rolling average quality score allowed over a window. </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="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
97
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<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qstepsize parameter allows you to set a number of bases to move the window over. Default=1.</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="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="90" 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">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.</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="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="91" 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">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qfile parameter allows you to provide a quality file.</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="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="92" 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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qthreshold parameter allows you to set a minimum quality score allowed. </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="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qaverage parameter allows you to set a minimum average quality score allowed. </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="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qwindowsize parameter allows you to set a number of bases in a window. Default=50.</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="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qwindowaverage parameter allows you to set a minimum average quality score allowed over a window. </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="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The rollaverage parameter allows you to set a minimum rolling average quality score allowed over a window. </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="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qstepsize parameter allows you to set a number of bases to move the window over. Default=1.</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="diff-line-num old_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
98
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<td class="diff-line-num new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The logtransform parameter allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform. Default=F.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">
99
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<td class="diff-line-num new_line 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: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The allfiles parameter will create separate group and fasta file for each grouping. The default is F.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">
100
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<td class="diff-line-num new_line 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: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The keepforward parameter allows you to indicate whether you want the forward primer removed or not. The default is F, meaning remove the forward primer.</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="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
101
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<td class="diff-line-num new_line 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: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qtrim parameter will trim sequence from the point that they fall below the qthreshold and put it in the .trim file if set to true. The default is T.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The keepfirst parameter trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements. </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="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
103
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<td class="diff-line-num new_line 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: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The removelast removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements.</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="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
104
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<td class="diff-line-num new_line 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: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The trim.seqs command should be in the following format: </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="diff-line-num old old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
105
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<td class="diff-line-num new_line 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: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, </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="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">helpString</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) </span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span></span>
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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
107
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<td class="diff-line-num new_line 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: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).</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="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
108
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<td class="diff-line-num new_line 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: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .</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="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
109
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<td class="diff-line-num new_line 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: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">helpString</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"getHelpString"</span><span class="p">);</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The allfiles parameter will create separate group and fasta file for each grouping. The default is F.</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="diff-line-num new old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="100" 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">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The keepforward parameter allows you to indicate whether you want the forward primer removed or not. The default is F, meaning remove the forward primer.</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="diff-line-num new old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The qtrim parameter will trim sequence from the point that they fall below the qthreshold and put it in the .trim file if set to true. The default is T.</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="diff-line-num new old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The keepfirst parameter trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements. </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="diff-line-num new old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The removelast removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements.</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="diff-line-num new old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"The trim.seqs command should be in the following format: </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="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, </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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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">helpString</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) </span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).</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="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">helpString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .</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="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">helpString</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="111" 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">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="112" 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">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"getHelpString"</span><span class="p">);</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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115
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"><span class="p">}</span></span>
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116
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//**********************************************************************************************************************</span></span>
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">TrimSeqsCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getOutputPattern</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">type</span><span class="p">)</span> <span class="p">{</span></span>
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118
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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120
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> </span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"qfile"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[filename],[tag],qual"</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right"> </span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[filename],[tag],fasta"</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right"> </span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"qfile"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[filename],[tag],qual"</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[filename],[tag],fasta"</span><span class="p">;</span> <span class="p">}</span></span>
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"group"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[filename],groups"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"name"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[filename],[tag],names"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"count"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[filename],[tag],count_table-[filename],count_table"</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="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -134,265 +134,265 @@ string TrimSeqsCommand::getOutputPattern(string type) {</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//***************************************************************************************************************</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"><span class="n" style="color: #333;">TrimSeqsCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TrimSeqsCommand</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">option</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"help"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">help</span><span class="p">();</span> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="n" style="color: #333;">calledHelp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"citation"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">citation</span><span class="p">();</span> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="n" style="color: #333;">calledHelp</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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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"help"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">help</span><span class="p">();</span> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="n" style="color: #333;">calledHelp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"citation"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">citation</span><span class="p">();</span> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="n" style="color: #333;">calledHelp</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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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"category"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="n" style="color: #333;">calledHelp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">OptionParser</span> <span class="n" style="color: #333;">parser</span><span class="p">(</span><span class="n" style="color: #333;">option</span><span class="p">,</span> <span class="n" style="color: #333;">setParameters</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">getParameters</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">ValidParameters</span> <span class="n" style="color: #333;">validParameter</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">fastaFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">validFile</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fastaFile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"not found"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff right"> </span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">fastaFile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">current</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getFastaFile</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff right"> </span></span>
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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
151
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<td class="diff-line-num new_line old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastaFile</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"Using "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fastaFile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" as input file for the fasta parameter.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
152
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<td class="diff-line-num new_line old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"You have no current fastafile and the fasta parameter is required.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="cpp"><span class="idiff left"> </span><span class="p"><span class="idiff">}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fastaFile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"not open"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abort</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">true</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff right"> </span></span>
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<td class="diff-line-num old old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setFastaFile</span><span class="p">(</span><span class="n" style="color: #333;">fastaFile</span><span class="p">);</span> <span class="p">}</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputdir</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span> <span class="n" style="color: #333;">outputdir</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">hasPath</span><span class="p">(</span><span class="n" style="color: #333;">fastaFile</span><span class="p">);</span> <span class="p">}</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//check for optional parameter and set defaults</span></span>
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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">// ...at some point should added some additional type checking...</span></span>
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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"flip"</span><span class="p">);</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"not found"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">flip</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">flip</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isTrue</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">validFile</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"oligos"</span><span class="p">);</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"not found"</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">oligoFile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"not open"</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abort</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">true</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff right"> </span></span>
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167
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<td class="diff-line-num new_line old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">oligoFile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">current</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">setOligosFile</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">oligoFile</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"maxambig"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-1"</span><span class="p">;</span> <span class="p">}</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mothurConvert</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxAmbig</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="144" 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">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">OptionParser</span> <span class="n" style="color: #333;">parser</span><span class="p">(</span><span class="n" style="color: #333;">option</span><span class="p">,</span> <span class="n" style="color: #333;">setParameters</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">getParameters</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" 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">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" 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">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">ValidParameters</span> <span class="n" style="color: #333;">validParameter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">fastaFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">validFile</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fastaFile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"not found"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="150" 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">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">fastaFile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">current</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getFastaFile</span></span><span class="p"><span class="idiff right">();</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastaFile</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"Using "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fastaFile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" as input file for the fasta parameter.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"You have no current fastafile and the fasta parameter is required.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="153" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"><span class="idiff left"> </span><span class="p"><span class="idiff">}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fastaFile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"not open"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abort</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">true</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">}</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setFastaFile</span><span class="p">(</span><span class="n" style="color: #333;">fastaFile</span><span class="p">);</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="155" 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">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputdir</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span> <span class="n" style="color: #333;">outputdir</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">hasPath</span><span class="p">(</span><span class="n" style="color: #333;">fastaFile</span><span class="p">);</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//check for optional parameter and set defaults</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">// ...at some point should added some additional type checking...</span></span>
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<td class="diff-line-num new new_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"flip"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"not found"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">flip</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">flip</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isTrue</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">validFile</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"oligos"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"not found"</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">oligoFile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"not open"</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abort</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">true</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">}</span></span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">oligoFile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">current</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">setOligosFile</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">oligoFile</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"maxambig"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-1"</span><span class="p">;</span> <span class="p">}</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mothurConvert</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxAmbig</span></span><span class="p"><span class="idiff right">);</span></span></span>
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172
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"maxhomop"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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174
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<td class="diff-line-num new_line old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mothurConvert</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxHomoP</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"maxhomop"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mothurConvert</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxHomoP</span></span><span class="p"><span class="idiff right">);</span></span></span>
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175
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"minlength"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span><span class="p">;</span> <span class="p">}</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">minLength</span><span class="p">);</span> </span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="cpp"> </span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"maxlength"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">maxLength</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="cpp"> </span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"bdiffs"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">bdiffs</span><span class="p">);</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="cpp"> </span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"pdiffs"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">pdiffs</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"minlength"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span><span class="p">;</span> <span class="p">}</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">minLength</span><span class="p">);</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"maxlength"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">maxLength</span><span class="p">);</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> </span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"bdiffs"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">bdiffs</span><span class="p">);</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> </span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"pdiffs"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">pdiffs</span><span class="p">);</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"ldiffs"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">ldiffs</span><span class="p">);</span></span>
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"> </span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left">ldiffs"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mothurConvert</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">l</span>diffs</span><span class="p">);</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left">sdiffs"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mothurConvert</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">s</span>diffs</span><span class="p">);</span></span>
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190
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"> </span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"sdiffs"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">sdiffs</span><span class="p">);</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="cpp"> </span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"tdiffs"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tempTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pdiffs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bdiffs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ldiffs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sdiffs</span><span class="p">;</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">tempTotal</span><span class="p">);</span> <span class="p">}</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">tdiffs</span><span class="p">);</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="cpp"> </span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tdiffs</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;">tdiffs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bdiffs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pdiffs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ldiffs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sdiffs</span><span class="p">;</span> <span class="p">}</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="cpp"> </span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">validFile</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"qfile"</span><span class="p">);</span> </span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span> <span class="p">}</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not open"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setQualFile</span><span class="p">(</span><span class="n" style="color: #333;">qFileName</span><span class="p">);</span> <span class="p">}</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp"> </span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">validFile</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">);</span> </span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">nameFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span> <span class="p">}</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not open"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">nameFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">nameFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setNameFile</span><span class="p">(</span><span class="n" style="color: #333;">nameFile</span><span class="p">);</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" 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">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"tdiffs"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tempTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pdiffs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bdiffs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ldiffs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sdiffs</span><span class="p">;</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">tempTotal</span><span class="p">);</span> <span class="p">}</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">tdiffs</span><span class="p">);</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> </span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tdiffs</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;">tdiffs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bdiffs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pdiffs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ldiffs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sdiffs</span><span class="p">;</span> <span class="p">}</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> </span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">validFile</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"qfile"</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not open"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" 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">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setQualFile</span><span class="p">(</span><span class="n" style="color: #333;">qFileName</span><span class="p">);</span> <span class="p">}</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="204" 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">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">validFile</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">nameFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span> <span class="p">}</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not open"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">nameFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" 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">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">nameFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setNameFile</span><span class="p">(</span><span class="n" style="color: #333;">nameFile</span><span class="p">);</span> <span class="p">}</span></span>
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208
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> </span>
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209
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">countfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">validFile</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"count"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
210
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<td class="diff-line-num new_line old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">countfile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"not open"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abort</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">true</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">countfile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff right"> </span></span>
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211
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<td class="diff-line-num new_line old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">countfile</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">countfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span> <span class="p">}</span></span>
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212
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<td class="diff-line-num new_line old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setCountFile</span><span class="p">(</span><span class="n" style="color: #333;">countfile</span><span class="p">);</span> <span class="p">}</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">countfile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"not open"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abort</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">true</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">countfile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">}</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="211" 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">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">countfile</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">countfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="212" 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">
212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setCountFile</span><span class="p">(</span><span class="n" style="color: #333;">countfile</span><span class="p">);</span> <span class="p">}</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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214
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">countfile</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">nameFile</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">))</span> <span class="p">{</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"You must enter ONLY ONE of the following: count or name.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> <span class="n" style="color: #333;">abort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"qthreshold"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">qThreshold</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"qtrim"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"t"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">qtrim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">isTrue</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"qthreshold"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">mothurConvert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">qThreshold</span><span class="p">);</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"qtrim"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"t"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">qtrim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">isTrue</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"rollaverage"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">qRollAverage</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"rollaverage"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">qRollAverage</span><span class="p">);</span></span>
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"qwindowaverage"</span><span class="p">);</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">qWindowAverage</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"qwindowaverage"</span><span class="p">);</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">qWindowAverage</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"qwindowsize"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"50"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">qWindowSize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"qwindowsize"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"50"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">qWindowSize</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"qstepsize"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">qWindowStep</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"qstepsize"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">qWindowStep</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"qaverage"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">qAverage</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"qaverage"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">qAverage</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"keepfirst"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">keepFirst</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">validParameter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">valid</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parameters</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"keepfirst"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">keepFirst</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"removelast"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">removeLast</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"allfiles"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"F"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">allFiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">isTrue</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"removelast"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">removeLast</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"allfiles"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"F"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">allFiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">isTrue</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"keepforward"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"F"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="n" style="color: #333;">keepforward</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">isTrue</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"logtransform"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"F"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">logtransform</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">isTrue</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left">keepforward"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"F"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff right">keepforward</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">isTrue</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left">checkorient"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"F"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff right">reorient</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">isTrue</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"logtransform"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"F"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">logtransform</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">isTrue</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"processors"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">){</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getProcessors</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">processors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setProcessors</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"> </span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">allFiles</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">oligoFile</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">)){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"You selected allfiles, but didn't enter an oligos. Ignoring the allfiles request.</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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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">qAverage</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;">qThreshold</span> <span class="o" style="font-weight: 600;">!=</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;">qFileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="262" 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">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"You didn't provide a quality file name, quality criteria will be ignored.</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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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="n" style="color: #333;">qAverage</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 new new_line" data-linenumber="264" 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">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="n" style="color: #333;">qThreshold</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 new new_line" data-linenumber="265" 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">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" 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">
266
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<pre style="margin: 0;">+<span id="LC266" 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;">flip</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">oligoFile</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">maxLength</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">minLength</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">maxAmbig</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">maxHomoP</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"You didn't set any options... quiting command.</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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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">abort</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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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="p">}</span></span>
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251
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<td class="diff-line-num new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp"> </span>
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<td class="diff-line-num old old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
252
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<td class="diff-line-num new_line old" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"checkorient"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"F"</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="cpp"> <span class="n" style="color: #333;">reorient</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">isTrue</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp"> </span>
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255
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<td class="diff-line-num new_line old" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validParameter</span><span class="p">.</span><span class="n" style="color: #333;">valid</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="s" style="color: #d14;">"processors"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"not found"</span><span class="p">){</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getProcessors</span><span class="p">();</span> <span class="p">}</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">processors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setProcessors</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"> </span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">allFiles</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">oligoFile</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">)){</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"You selected allfiles, but didn't enter an oligos. Ignoring the allfiles request.</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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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp"> <span class="p">}</span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">qAverage</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;">qThreshold</span> <span class="o" style="font-weight: 600;">!=</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;">qFileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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262
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<td class="diff-line-num new_line old" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"You didn't provide a quality file name, quality criteria will be ignored.</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="diff-line-num old old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp"> <span class="n" style="color: #333;">qAverage</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 old old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
264
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<td class="diff-line-num new_line old" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"> <span class="n" style="color: #333;">qThreshold</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 old old_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
266
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<pre style="margin: 0;">-<span id="LC266" 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;">flip</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">oligoFile</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">maxLength</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">minLength</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">maxAmbig</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">maxHomoP</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span> </span>
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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">
267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"You didn't set any options... quiting command.</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="diff-line-num old old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">abort</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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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="cpp"> <span class="p">}</span></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp"> </span>
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271
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">countfile</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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272
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nameFile</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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273
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273
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<pre style="margin: 0;"> <span id="LC273" 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;">string</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;">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;">fastaFile</span><span class="p">);</span></span>
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<td class="diff-line-num 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: 0 5px;" align="right" bgcolor="#fafafa">
274
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274
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<pre style="margin: 0;"> <span id="LC274" 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;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getMothurCalling</span><span class="p">())</span> <span class="p">{</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">getNameFile</span><span class="p">(</span><span class="n" style="color: #333;">files</span><span class="p">);</span> <span class="p">}</span></span>
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275
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"> <span class="p">}</span></span>
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276
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"> <span class="p">}</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">pairedOligos</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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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">createGroup</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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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//***************************************************************************************************************</span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">TrimSeqsCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">execute</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">abort</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">calledHelp</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variables</span><span class="p">;</span><span class="idiff left right"> </span></span>
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">variables</span><span class="p">[</span><span class="s" style="color: #d14;">"[filename]"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputdir</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">getRootName</span><span class="p">(</span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">getSimpleName</span><span class="p">(</span><span class="n" style="color: #333;">fastaFile</span><span class="p">));</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span><span class="p">{</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">abort</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">calledHelp</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variables</span><span class="p">;</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">variables</span><span class="p">[</span><span class="s" style="color: #d14;">"[filename]"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputdir</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">getRootName</span><span class="p">(</span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">getSimpleName</span><span class="p">(</span><span class="n" style="color: #333;">fastaFile</span><span class="p">));</span></span>
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297
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">variables</span><span class="p">[</span><span class="s" style="color: #d14;">"[tag]"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"trim"</span><span class="p">;</span></span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimSeqFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimSeqFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="299" 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">
299
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimQualFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"qfile"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimSeqFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimSeqFile</span><span class="p">);</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimSeqFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimSeqFile</span><span class="p">);</span></span>
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301
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> </span>
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302
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">variables</span><span class="p">[</span><span class="s" style="color: #d14;">"[tag]"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"scrap"</span><span class="p">;</span></span>
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303
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<td class="diff-line-num new_line old" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapSeqFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="303" 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">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapSeqFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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304
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304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapQualFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"qfile"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapSeqFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapSeqFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimQualFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapQualFile</span><span class="p">);</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"qfile"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimQualFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"qfile"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapQualFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapSeqFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapSeqFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimQualFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapQualFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"qfile"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimQualFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"qfile"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapQualFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">variables</span><span class="p">[</span><span class="s" style="color: #d14;">"[filename]"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputdir</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">getRootName</span><span class="p">(</span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">getSimpleName</span><span class="p">(</span><span class="n" style="color: #333;">nameFile</span><span class="p">));</span></span>
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="n" style="color: #333;">variables</span><span class="p">[</span><span class="s" style="color: #d14;">"[tag]"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"trim"</span><span class="p">;</span></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimNameFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimNameFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">variables</span><span class="p">[</span><span class="s" style="color: #d14;">"[tag]"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"scrap"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapNameFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nameFile</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">readNames</span><span class="p">(</span><span class="n" style="color: #333;">nameFile</span><span class="p">,</span> <span class="n" style="color: #333;">nameMap</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimNameFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapNameFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"name"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimNameFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"name"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapNameFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapNameFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nameFile</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">readNames</span><span class="p">(</span><span class="n" style="color: #333;">nameFile</span><span class="p">,</span> <span class="n" style="color: #333;">nameMap</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimNameFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapNameFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"name"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimNameFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"name"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapNameFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"> </span>
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">variables</span><span class="p">[</span><span class="s" style="color: #d14;">"[filename]"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputdir</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">getRootName</span><span class="p">(</span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">getSimpleName</span><span class="p">(</span><span class="n" style="color: #333;">countfile</span><span class="p">));</span></span>
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">variables</span><span class="p">[</span><span class="s" style="color: #d14;">"[tag]"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"trim"</span><span class="p">;</span></span>
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326
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimCountFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"count"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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327
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">variables</span><span class="p">[</span><span class="s" style="color: #d14;">"[tag]"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"scrap"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapCountFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"count"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">countfile</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapCountFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getOutputFileName</span><span class="p">(</span><span class="s" style="color: #d14;">"count"</span><span class="p">,</span><span class="n" style="color: #333;">variables</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">countfile</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">CountTable</span> <span class="n" style="color: #333;">ct</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp"> <span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">readTable</span><span class="p">(</span><span class="n" style="color: #333;">countfile</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp"> <span class="n" style="color: #333;">nameCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">getNameMap</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimCountFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapCountFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"count"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimCountFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"count"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapCountFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimCountFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapCountFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"count"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">trimCountFile</span><span class="p">);</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">[</span><span class="s" style="color: #d14;">"count"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scrapCountFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getControl_pressed</span><span class="p">())</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</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="LC339" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getControl_pressed</span><span class="p">())</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</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="LC339" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">startTime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">numSeqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">createProcessesCreateTrim</span><span class="p">(</span><span class="n" style="color: #333;">fastaFile</span><span class="p">,</span> <span class="n" style="color: #333;">qFileName</span><span class="p">,</span> <span class="n" style="color: #333;">trimSeqFile</span><span class="p">,</span> <span class="n" style="color: #333;">scrapSeqFile</span><span class="p">,</span> <span class="n" style="color: #333;">trimQualFile</span><span class="p">,</span> <span class="n" style="color: #333;">scrapQualFile</span><span class="p">,</span> <span class="n" style="color: #333;">trimNameFile</span><span class="p">,</span> <span class="n" style="color: #333;">scrapNameFile</span><span class="p">,</span> <span class="n" style="color: #333;">trimCountFile</span><span class="p">,</span> <span class="n" style="color: #333;">scrapCountFile</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"It took "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">startTime</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" secs to trim "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">numSeqs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" sequences.</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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<pre style="margin: 0;">-<span id="LC345" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getControl_pressed</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">outputNames</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mothurRemove</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputNames</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]);</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getControl_pressed</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">outputNames</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mothurRemove</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputNames</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]);</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//output group counts</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOutEndLine</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">total</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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<pre style="margin: 0;">-<span id="LC351" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">groupCounts</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;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"Group count: </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">total</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">it</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">second</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOut</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">it</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">first</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">toString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">it</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">second</span></span><span class="p"><span class="idiff">));</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOutEndLine</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff right"> </span></span>
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354
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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355
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"Total of all groups is "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">total</span><span class="p">));</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOutEndLine</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getControl_pressed</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">outputNames</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mothurRemove</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputNames</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]);</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//output group counts</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOutEndLine</span><span class="p">();</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">total</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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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">groupCounts</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;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"Group count: </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> <span class="p">}</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">total</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">it</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">second</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOut</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">it</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">first</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">toString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">it</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">second</span></span><span class="p"><span class="idiff">));</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOutEndLine</span></span><span class="p"><span class="idiff right">();</span></span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"Total of all groups is "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">total</span><span class="p">));</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOutEndLine</span><span class="p">();</span> <span class="p">}</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getControl_pressed</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">outputNames</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mothurRemove</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputNames</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]);</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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358
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="cpp"></span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//set fasta file as new current fastafile</span></span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">currentName</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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361
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
362
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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363
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<td class="diff-line-num new_line old" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">currentName</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setFastaFile</span><span class="p">(</span><span class="n" style="color: #333;">currentName</span><span class="p">);</span> <span class="p">}</span></span>
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364
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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365
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"name"</span><span class="p">);</span></span>
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367
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<td class="diff-line-num new_line old" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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368
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">currentName</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setNameFile</span><span class="p">(</span><span class="n" style="color: #333;">currentName</span><span class="p">);</span> <span class="p">}</span></span>
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369
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"qfile"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">currentName</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setQualFile</span><span class="p">(</span><span class="n" style="color: #333;">currentName</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"group"</span><span class="p">);</span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">currentName</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setGroupFile</span><span class="p">(</span><span class="n" style="color: #333;">currentName</span><span class="p">);</span> <span class="p">}</span></span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//set fasta file as new current fastafile</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">currentName</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="362" 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">
362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">currentName</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setFastaFile</span><span class="p">(</span><span class="n" style="color: #333;">currentName</span><span class="p">);</span> <span class="p">}</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"name"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">currentName</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setNameFile</span><span class="p">(</span><span class="n" style="color: #333;">currentName</span><span class="p">);</span> <span class="p">}</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"qfile"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">currentName</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setQualFile</span><span class="p">(</span><span class="n" style="color: #333;">currentName</span><span class="p">);</span> <span class="p">}</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"group"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">currentName</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setGroupFile</span><span class="p">(</span><span class="n" style="color: #333;">currentName</span><span class="p">);</span> <span class="p">}</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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380
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"> </span>
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381
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"count"</span><span class="p">);</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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383
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<td class="diff-line-num new_line old" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">currentName</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setCountFile</span><span class="p">(</span><span class="n" style="color: #333;">currentName</span><span class="p">);</span> <span class="p">}</span></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="382" 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">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">outputTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="383" 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">
383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">currentName</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">itTypes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setCountFile</span><span class="p">(</span><span class="n" style="color: #333;">currentName</span><span class="p">);</span> <span class="p">}</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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385
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"></span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOut</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">Output File Names: </span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">outputNames</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOut</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputNames</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOutEndLine</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"execute"</span><span class="p">);</span></span>
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394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOut</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">Output File Names: </span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff right">);</span></span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">outputNames</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOut</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputNames</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOutEndLine</span><span class="p">();</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">;</span></span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"execute"</span><span class="p">);</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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396
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"><span class="p">}</span></span>
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//***************************************************************************************************************</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp"></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">@@ -423,31 +423,31 @@ bool removeLastTrim(Sequence& sequence, QualityScores& qscores, int removeLast){</td>
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//***************************************************************************************************************</span></span>
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">cullLength</span><span class="p">(</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minLength</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxLength</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">getNumBases</span><span class="p">();</span></span>
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426
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//guilty until proven innocent</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//guilty until proven innocent</span></span>
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp"> </span>
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428
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minLength</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">maxLength</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minLength</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxLength</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minLength</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">maxLength</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minLength</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxLength</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//***************************************************************************************************************</span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">cullHomoP</span><span class="p">(</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxHomoP</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">longHomoP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">getLongHomoPolymer</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//guilty until proven innocent</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//guilty until proven innocent</span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">longHomoP</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxHomoP</span><span class="p">){</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">longHomoP</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxHomoP</span><span class="p">){</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//***************************************************************************************************************</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">cullAmbigs</span><span class="p">(</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxAmbig</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numNs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">getAmbigBases</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//guilty until proven innocent</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//guilty until proven innocent</span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numNs</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxAmbig</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numNs</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxAmbig</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -541,27 +541,27 @@ struct trimData {</td>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**************************************************************************************/</span></span>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//string filename, string qFileName, string trimFileName, string scrapFileName, string trimQFileName, string scrapQFileName, string trimNFileName, string scrapNFileName, string trimCFileName, string scrapCFileName, string groupFileName, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames, linePair line, linePair qline</span></span>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">driverTrim</span><span class="p">(</span><span class="n" style="color: #333;">trimData</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">params</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numFPrimers</span><span class="p">,</span> <span class="n" style="color: #333;">numRPrimers</span><span class="p">,</span> <span class="n" style="color: #333;">numLinkers</span><span class="p">,</span> <span class="n" style="color: #333;">numSpacers</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"> <span class="n" style="color: #333;">numFPrimers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp"> <span class="n" style="color: #333;">numRPrimers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">revPrimer</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="cpp"> <span class="n" style="color: #333;">numLinkers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">linker</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cpp"> <span class="n" style="color: #333;">numSpacers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">spacer</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">inFASTA</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">openInputFile</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">inFASTA</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">inFASTA</span><span class="p">.</span><span class="n" style="color: #333;">seekg</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineStart</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">qFile</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qFileName</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">openInputFile</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qFileName</span><span class="p">,</span> <span class="n" style="color: #333;">qFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">qFile</span><span class="p">.</span><span class="n" style="color: #333;">seekg</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qlineStart</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">moreSeqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">inFASTA</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">openInputFile</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">inFASTA</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">inFASTA</span><span class="p">.</span><span class="n" style="color: #333;">seekg</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineStart</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">qFile</span><span class="p">;</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qFileName</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">openInputFile</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qFileName</span><span class="p">,</span> <span class="n" style="color: #333;">qFile</span><span class="p">);</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">qFile</span><span class="p">.</span><span class="n" style="color: #333;">seekg</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qlineStart</span><span class="p">);</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">moreSeqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numBarcodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">barcodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">TrimOligos</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">trimOligos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">TrimOligos</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">trimOligos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pairedOligos</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">trimOligos</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TrimOligos</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pdiffs</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bdiffs</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="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pairedPrimers</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pairedBarcodes</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="n" style="color: #333;">numBarcodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pairedBarcodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">numFPrimers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pairedPrimers</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">trimOligos</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TrimOligos</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pdiffs</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bdiffs</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ldiffs</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sdiffs</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">primers</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">barcodes</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">revPrimer</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">linker</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">spacer</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="cpp"> </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">@@ -594,42 +594,42 @@ int driverTrim(trimData* params) {</td>
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numBarcodes</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;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">createGroup</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>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">moreSeqs</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">moreSeqs</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">obsBDiffs</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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<pre style="margin: 0;"> <span id="LC600" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">obsPDiffs</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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<pre style="margin: 0;"> <span id="LC601" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getControl_pressed</span><span class="p">())</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">}</span></span>
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603
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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604
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">success</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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605
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trashCode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getControl_pressed</span><span class="p">())</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">}</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">success</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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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trashCode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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606
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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;">string</span> <span class="n" style="color: #333;">commentString</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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607
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">currentSeqsDiffs</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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<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">currentSeqsDiffs</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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608
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608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="cpp"></span>
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609
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">currSeq</span><span class="p">(</span><span class="n" style="color: #333;">inFASTA</span><span class="p">);</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">gobble</span><span class="p">(</span><span class="n" style="color: #333;">inFASTA</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="idiff left right"> </span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">currSeq</span><span class="p">(</span><span class="n" style="color: #333;">inFASTA</span><span class="p">);</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">gobble</span><span class="p">(</span><span class="n" style="color: #333;">inFASTA</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="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">savedSeq</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">(),</span> <span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">getAligned</span><span class="p">());</span></span>
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611
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="cpp"> </span>
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612
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">QualityScores</span> <span class="n" style="color: #333;">currQual</span><span class="p">;</span> <span class="n" style="color: #333;">QualityScores</span> <span class="n" style="color: #333;">savedQual</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 class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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614
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">currQual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">QualityScores</span><span class="p">(</span><span class="n" style="color: #333;">qFile</span><span class="p">);</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">gobble</span><span class="p">(</span><span class="n" style="color: #333;">qFile</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="idiff left right"> </span><span class="n" style="color: #333;">QualityScores</span> <span class="n" style="color: #333;">currQual</span><span class="p">;</span> <span class="n" style="color: #333;">QualityScores</span> <span class="n" style="color: #333;">savedQual</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">currQual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">QualityScores</span><span class="p">(</span><span class="n" style="color: #333;">qFile</span><span class="p">);</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">gobble</span><span class="p">(</span><span class="n" style="color: #333;">qFile</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="cpp"> <span class="n" style="color: #333;">savedQual</span><span class="p">.</span><span class="n" style="color: #333;">setName</span><span class="p">(</span><span class="n" style="color: #333;">currQual</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">());</span> <span class="n" style="color: #333;">savedQual</span><span class="p">.</span><span class="n" style="color: #333;">setScores</span><span class="p">(</span><span class="n" style="color: #333;">currQual</span><span class="p">.</span><span class="n" style="color: #333;">getScores</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="cpp"><span class="idiff left right"> </span> </span>
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">origSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">getUnaligned</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">origSeq</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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621
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">barcodeIndex</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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<pre style="margin: 0;">-<span id="LC622" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">primerIndex</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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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp"><span class="idiff left right"> </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="idiff left right"> </span> </span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">origSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">getUnaligned</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">origSeq</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">barcodeIndex</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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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">primerIndex</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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<pre style="margin: 0;"> <span id="LC623" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numLinkers</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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<pre style="margin: 0;">-<span id="LC625" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripLinker</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ldiffs</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'k'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </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="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="n" style="color: #333;">currentSeqsDiffs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">success</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripLinker</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">);</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ldiffs</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'k'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </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="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="n" style="color: #333;">currentSeqsDiffs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">success</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="cpp"></span>
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629
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"><span class="idiff left right"> </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>
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631
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numBarcodes</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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632
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="cpp"><span class="idiff left right"> </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="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripBarcode</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">,</span> <span class="n" style="color: #333;">barcodeIndex</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="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numBarcodes</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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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"><span class="idiff left right"> </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="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripBarcode</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">,</span> <span class="n" style="color: #333;">barcodeIndex</span><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="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pairedOligos</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;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</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;">results</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="n" style="color: #333;">commentString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"fbdiffs="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">results</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="s" style="color: #d14;">"("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getCodeValue</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bdiffs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"), rbdiffs="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">2</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;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getCodeValue</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bdiffs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">") "</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -638,20 +638,20 @@ int driverTrim(trimData* params) {</td>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="cpp"> <span class="n" style="color: #333;">commentString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"bdiffs="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">results</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="s" style="color: #d14;">"("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getCodeValue</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bdiffs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">") "</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">bdiffs</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span> <span class="n" style="color: #333;">trashCode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sc" style="color: #d14;">'b'</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="n" style="color: #333;">currentSeqsDiffs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">success</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">bdiffs</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span> <span class="n" style="color: #333;">trashCode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sc" style="color: #d14;">'b'</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="n" style="color: #333;">currentSeqsDiffs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">success</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="cpp"> <span class="n" style="color: #333;">obsBDiffs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC645" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numSpacers</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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647
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripSpacer</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sdiffs</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'s'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="n" style="color: #333;">currentSeqsDiffs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">success</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripSpacer</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sdiffs</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'s'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="n" style="color: #333;">currentSeqsDiffs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">success</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numFPrimers</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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<pre style="margin: 0;">-<span id="LC654" class="line" lang="cpp"><span class="idiff left right"> </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="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripForward</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">,</span> <span class="n" style="color: #333;">primerIndex</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">keepforward</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numFPrimers</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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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp"><span class="idiff left right"> </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="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripForward</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">,</span> <span class="n" style="color: #333;">primerIndex</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">keepforward</span><span class="p">);</span></span>
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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;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pairedOligos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</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;">results</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="cpp"> <span class="n" style="color: #333;">commentString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"fpdiffs="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">results</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="s" style="color: #d14;">"("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getCodeValue</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pdiffs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"), rpdiffs="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">2</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;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getCodeValue</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pdiffs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">") "</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">@@ -660,20 +660,20 @@ int driverTrim(trimData* params) {</td>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="cpp"> <span class="n" style="color: #333;">commentString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"fpdiffs="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">results</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="s" style="color: #d14;">"("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getCodeValue</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pdiffs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">") "</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">pdiffs</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span> <span class="n" style="color: #333;">trashCode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="n" style="color: #333;">currentSeqsDiffs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">success</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">pdiffs</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span> <span class="n" style="color: #333;">trashCode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="n" style="color: #333;">currentSeqsDiffs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">success</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="cpp"> <span class="n" style="color: #333;">obsPDiffs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numRPrimers</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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<pre style="margin: 0;">-<span id="LC669" class="line" lang="cpp"><span class="idiff left right"> </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="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripReverse</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">);</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numRPrimers</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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<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp"><span class="idiff left right"> </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="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripReverse</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="cpp"> <span class="n" style="color: #333;">commentString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"rpdiffs="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">results</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="s" style="color: #d14;">"("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">trimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getCodeValue</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pdiffs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">") "</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pdiffs</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'r'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pdiffs</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'r'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="n" style="color: #333;">currentSeqsDiffs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">success</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">currentSeqsDiffs</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tdiffs</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">trashCode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">currentSeqsDiffs</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tdiffs</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">trashCode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">;</span> <span class="p">}</span></span>
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677
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677
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="cpp"> </span>
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678
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">reorient</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">trashCode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//if you failed and want to check the reverse</span></span>
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679
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thisSuccess</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="694" 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="694" 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">@@ -694,7 +694,7 @@ int driverTrim(trimData* params) {</td>
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694
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="cpp"> <span class="n" style="color: #333;">thisSuccess</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="cpp"> <span class="n" style="color: #333;">thiscommentString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"bdiffs="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">results</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="s" style="color: #d14;">"("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rtrimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getCodeValue</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bdiffs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">") "</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="cpp"> <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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">thisSuccess</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bdiffs</span><span class="p">)</span><span class="idiff left right"> </span><span class="p">{</span> <span class="n" style="color: #333;">thisTrashCode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"b"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">thisSuccess</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bdiffs</span><span class="p">)</span><span class="idiff left right"> </span><span class="p">{</span> <span class="n" style="color: #333;">thisTrashCode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"b"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="n" style="color: #333;">thisCurrentSeqsDiffs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">thisSuccess</span><span class="p">;</span> <span class="p">}</span></span>
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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>
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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">@@ -710,12 +710,12 @@ int driverTrim(trimData* params) {</td>
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710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="cpp"> <span class="n" style="color: #333;">thisSuccess</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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711
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711
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="cpp"> <span class="n" style="color: #333;">thiscommentString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"pdiffs="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">results</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="s" style="color: #d14;">"("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rtrimOligos</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getCodeValue</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pdiffs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">") "</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="cpp"> <span class="p">}</span></span>
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713
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">thisSuccess</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pdiffs</span><span class="p">)</span><span class="idiff left right"> </span><span class="p">{</span> <span class="n" style="color: #333;">thisTrashCode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"f"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">thisSuccess</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pdiffs</span><span class="p">)</span><span class="idiff left right"> </span><span class="p">{</span> <span class="n" style="color: #333;">thisTrashCode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"f"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="n" style="color: #333;">thisCurrentSeqsDiffs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">thisSuccess</span><span class="p">;</span> <span class="p">}</span></span>
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715
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715
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="cpp"> <span class="p">}</span></span>
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716
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">revPDiffs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisSuccess</span><span class="p">;</span></span>
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717
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717
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="cpp"></span>
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718
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">thisCurrentSeqsDiffs</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tdiffs</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">thisTrashCode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">;</span> <span class="p">}</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">thisCurrentSeqsDiffs</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tdiffs</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">thisTrashCode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">;</span> <span class="p">}</span></span>
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719
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="cpp"> </span>
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<td class="diff-line-num old_line" data-linenumber="720" 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">
720
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">thisTrashCode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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721
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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;">obsPDiffs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">revPDiffs</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -736,46 +736,46 @@ int driverTrim(trimData* params) {</td>
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736
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736
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">trashCode</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;">thisTrashCode</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")"</span><span class="p">;</span> <span class="p">}</span></span>
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737
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737
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="cpp"> <span class="p">}</span></span>
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738
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738
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="cpp"> </span>
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<td class="diff-line-num old old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
739
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">keepFirst</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;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">keepFirstTrim</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">keepFirst</span><span class="p">);</span> <span class="p">}</span></span>
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740
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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741
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">removeLast</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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742
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<pre style="margin: 0;">-<span id="LC742" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">removeLastTrim</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">removeLast</span><span class="p">);</span></span>
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743
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<pre style="margin: 0;">-<span id="LC743" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'l'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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744
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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745
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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746
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">origLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">getNumBases</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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749
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isEqual</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qThreshold</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">))</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">currQual</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stripQualThreshold</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">currSeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qThreshold</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isEqual</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qAverage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">currQual</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">cullQualAverage</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">currSeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qAverage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">logtransform</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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751
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isEqual</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qRollAverage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">currQual</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stripQualRollingAverage</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">currSeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qRollAverage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">logtransform</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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752
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<pre style="margin: 0;">-<span id="LC752" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isEqual</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qWindowAverage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">)){</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">currQual</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stripQualWindowAverage</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">currSeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qWindowStep</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qWindowSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qWindowAverage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">logtransform</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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753
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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754
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<pre style="margin: 0;">-<span id="LC754" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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755
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//you don't want to trim, if it fails above then scrap it</span></span>
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756
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="cpp"><span class="idiff left right"> </span><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;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qtrim</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">origLength</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">getNumBases</span><span class="p">()))</span> <span class="p">{</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>
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757
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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758
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<pre style="margin: 0;">-<span id="LC758" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'q'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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759
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="cpp"><span class="idiff left"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff right"> </span></span>
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760
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num old old_line" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
761
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minLength</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;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxLength</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 old old_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
762
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cullLength</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minLength</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxLength</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
763
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'l'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
764
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
765
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxHomoP</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 old old_line" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
766
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cullHomoP</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxHomoP</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
767
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'h'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
768
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
769
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxAmbig</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>
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770
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cullAmbigs</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxAmbig</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
771
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'n'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
772
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
773
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC773" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num old old_line" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
774
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">flip</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff right"> </span><span class="c1" style="color: #998; font-style: italic;">// should go last</span></span>
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<td class="diff-line-num old old_line" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
775
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">reverseComplement</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
776
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qFileName</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">currQual</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">flipQScores</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff right"> </span> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
777
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<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">keepFirst</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;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">keepFirstTrim</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">keepFirst</span><span class="p">);</span> <span class="p">}</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">removeLast</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 new new_line" data-linenumber="742" 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">
742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">removeLastTrim</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">currQual</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">removeLast</span><span class="p">);</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'l'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">origLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">getNumBases</span><span class="p">();</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isEqual</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qThreshold</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">))</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">currQual</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stripQualThreshold</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">currSeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qThreshold</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isEqual</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qAverage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">currQual</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">cullQualAverage</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">currSeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qAverage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">logtransform</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isEqual</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qRollAverage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">currQual</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stripQualRollingAverage</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">currSeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qRollAverage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">logtransform</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isEqual</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qWindowAverage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">)){</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">currQual</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stripQualWindowAverage</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">currSeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qWindowStep</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qWindowSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qWindowAverage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">logtransform</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="755" 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">
755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//you don't want to trim, if it fails above then scrap it</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="cpp"><span class="idiff left right"> </span><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;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qtrim</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">origLength</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">getNumBases</span><span class="p">()))</span> <span class="p">{</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="758" 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">
758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'q'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="cpp"><span class="idiff left"> </span><span class="p"><span class="idiff right">}</span></span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minLength</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;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxLength</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 new new_line" data-linenumber="762" 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">
762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cullLength</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minLength</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxLength</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="763" 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">
763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'l'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="765" 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">
765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxHomoP</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 new new_line" data-linenumber="766" 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">
766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cullHomoP</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxHomoP</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="767" 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">
767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'h'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxAmbig</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>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cullAmbigs</span><span class="p">(</span><span class="n" style="color: #333;">currSeq</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxAmbig</span><span class="p">);</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">success</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trashCode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'n'</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">flip</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff right"> </span><span class="c1" style="color: #998; font-style: italic;">// should go last</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">reverseComplement</span><span class="p">();</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qFileName</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">currQual</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">flipQScores</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff right"> </span> <span class="p">}</span></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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779
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779
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDebug</span><span class="p">())</span> <span class="p">{</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"[DEBUG]: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">", trashcode= "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">trashCode</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 class="p">}</span></span>
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780
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780
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="cpp"></span>
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781
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781
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seqComment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">getComment</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="797" 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="797" 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">@@ -797,7 +797,7 @@ int driverTrim(trimData* params) {</td>
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797
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797
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="cpp"> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">groupMap</span><span class="p">[</span><span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">()]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisGroup</span><span class="p">;</span></span>
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798
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798
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="cpp"> </span>
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799
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799
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">thisGroup</span><span class="p">);</span></span>
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800
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<pre style="margin: 0;">-<span id="LC800" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span><span class="idiff left right"> </span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">groupCounts</span><span class="p">[</span><span class="n" style="color: #333;">thisGroup</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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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span><span class="idiff left right"> </span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">groupCounts</span><span class="p">[</span><span class="n" style="color: #333;">thisGroup</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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801
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">groupCounts</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</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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802
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="cpp"> <span class="p">}</span></span>
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803
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="810" 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="810" 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">@@ -810,39 +810,39 @@ int driverTrim(trimData* params) {</td>
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810
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="cpp"> <span class="n" style="color: #333;">currSeq</span><span class="p">.</span><span class="n" style="color: #333;">printSequence</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scrapFileName</span><span class="p">);</span></span>
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811
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span> <span class="n" style="color: #333;">currQual</span><span class="p">.</span><span class="n" style="color: #333;">printQScores</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scrapQFileName</span><span class="p">);</span> <span class="p">}</span></span>
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812
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812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="cpp"> <span class="p">}</span></span>
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813
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<pre style="margin: 0;">-<span id="LC813" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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814
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<pre style="margin: 0;">-<span id="LC814" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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815
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<pre style="margin: 0;">-<span id="LC815" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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816
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<pre style="margin: 0;">-<span id="LC816" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#if defined NON_WINDOWS</span></span>
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817
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<pre style="margin: 0;">-<span id="LC817" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inFASTA</span><span class="p">.</span><span class="n" style="color: #333;">tellg</span><span class="p">();</span></span>
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818
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<pre style="margin: 0;">-<span id="LC818" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">pos</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="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineEnd</span><span class="p">))</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">}</span></span>
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819
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<pre style="margin: 0;">-<span id="LC819" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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820
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<td class="diff-line-num new_line old" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC820" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineEnd</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">inFASTA</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">()))</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">}</span></span>
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821
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<pre style="margin: 0;">-<span id="LC821" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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822
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<pre style="margin: 0;">-<span id="LC822" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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823
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<pre style="margin: 0;">-<span id="LC823" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//report progress</span></span>
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824
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<pre style="margin: 0;">-<span id="LC824" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">count</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1000</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOutJustToScreen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">toString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">count</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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825
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<td class="diff-line-num new_line old" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num old old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
826
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<td class="diff-line-num new_line old" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
827
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<td class="diff-line-num new_line old" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//report progress</span></span>
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828
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<td class="diff-line-num new_line old" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">count</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1000</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOutJustToScreen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">toString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">count</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
829
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<td class="diff-line-num new_line old" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num old old_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
830
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<td class="diff-line-num new_line old" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">trimOligos</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="813" 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">
813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="814" 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">
814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="815" 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">
815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="816" 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">
816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#if defined NON_WINDOWS</span></span>
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<td class="diff-line-num new new_line" data-linenumber="817" 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">
817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inFASTA</span><span class="p">.</span><span class="n" style="color: #333;">tellg</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="818" 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">
818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">pos</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="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineEnd</span><span class="p">))</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="819" 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">
819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="820" 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">
820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineEnd</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">inFASTA</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">()))</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="821" 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">
821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num new new_line" data-linenumber="822" 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">
822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="823" 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">
823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//report progress</span></span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">count</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1000</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOutJustToScreen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">toString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">count</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="825" 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">
825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="826" 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">
826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="827" 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">
827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//report progress</span></span>
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<td class="diff-line-num new new_line" data-linenumber="828" 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">
828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">count</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1000</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOutJustToScreen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">toString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">count</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="829" 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">
829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="cpp"><span class="idiff left right"> </span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="830" 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">
830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">trimOligos</span><span class="p">;</span></span>
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831
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<td class="diff-line-num new_line" data-linenumber="831" 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">
831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">reorient</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">rtrimOligos</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
832
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<td class="diff-line-num new_line old" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC832" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">inFASTA</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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833
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<td class="diff-line-num new_line old" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qFileName</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qFile</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">close</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="832" 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">
832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">inFASTA</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="833" 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">
833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qFileName</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qFile</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">close</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="834" 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">
834
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<td class="diff-line-num new_line" data-linenumber="834" 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">
834
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="cpp"> </span>
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835
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<td class="diff-line-num new_line" data-linenumber="835" 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">
835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="836" 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">
836
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<td class="diff-line-num new_line" data-linenumber="836" 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">
836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
837
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<td class="diff-line-num new_line old" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC837" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
838
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<td class="diff-line-num new_line old" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC838" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"driverTrim"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
839
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<td class="diff-line-num new_line old" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"driverTrim"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**************************************************************************************************/</span></span>
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">TrimSeqsCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">createProcessesCreateTrim</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">qFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimFASTAFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapFASTAFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimQualFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapQualFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimNameFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapNameFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimCountFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapCountFileName</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC845" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">groupFile</span><span class="p">;</span></span>
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847
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<pre style="margin: 0;"> <span id="LC847" class="line" lang="cpp"> <span class="n" style="color: #333;">Oligos</span> <span class="n" style="color: #333;">oligos</span><span class="p">;</span></span>
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848
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848
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">oligoFile</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -917,7 +917,7 @@ long long TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFi</td>
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<pre style="margin: 0;"> <span id="LC917" class="line" lang="cpp"> </span>
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918
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918
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<pre style="margin: 0;"> <span id="LC918" class="line" lang="cpp"> <span class="n" style="color: #333;">set</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;">badNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">badNames</span><span class="p">;</span></span>
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919
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<pre style="margin: 0;"> <span id="LC919" class="line" lang="cpp"> <span class="n" style="color: #333;">groupCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">groupCounts</span><span class="p">;</span></span>
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920
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<pre style="margin: 0;">-<span id="LC920" class="line" lang="cpp"> <span class="n" style="color: #333;">groupMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">groupMap</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">map</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right"> </span><span class="n" style="color: #333;">groupMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">groupMap</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC921" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC922" 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;">processors</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="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="cpp"> <span class="n" style="color: #333;">workerThreads</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;">join</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">@@ -953,11 +953,11 @@ long long TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFi</td>
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<pre style="margin: 0;"> <span id="LC953" class="line" lang="cpp"> <span class="n" style="color: #333;">processNamesCountFiles</span><span class="p">(</span><span class="n" style="color: #333;">trimFASTAFileName</span><span class="p">,</span> <span class="n" style="color: #333;">badNames</span><span class="p">,</span> <span class="n" style="color: #333;">groupMap</span><span class="p">,</span> <span class="n" style="color: #333;">trimNameFileName</span><span class="p">,</span> <span class="n" style="color: #333;">scrapNameFileName</span><span class="p">,</span> <span class="n" style="color: #333;">trimCountFileName</span><span class="p">,</span> <span class="n" style="color: #333;">scrapCountFileName</span><span class="p">,</span> <span class="n" style="color: #333;">groupFile</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">num</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC956" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC957" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC958" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"createProcessesCreateTrim"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC959" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC960" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"createProcessesCreateTrim"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**************************************************************************************************/</span></span>
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">TrimSeqsCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">processNamesCountFiles</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimFasta</span><span class="p">,</span> <span class="n" style="color: #333;">set</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;">badNames</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">groupMap</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimNameFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapNameFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimCountFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapCountFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">groupFile</span><span class="p">)</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">@@ -1007,7 +1007,7 @@ int TrimSeqsCommand::processNamesCountFiles(string trimFasta, set<string> badNam</td>
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1007
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<pre style="margin: 0;"> <span id="LC1007" class="line" lang="cpp"> <span class="n" style="color: #333;">outGroup</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">itGroup</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">itGroup</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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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1008
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1008
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<pre style="margin: 0;"> <span id="LC1008" class="line" lang="cpp"> <span class="p">}</span></span>
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1009
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1009
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<pre style="margin: 0;"> <span id="LC1009" class="line" lang="cpp"> <span class="n" style="color: #333;">outGroup</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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1010
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<pre style="margin: 0;">-<span id="LC1010" 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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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">countfile</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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1011
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1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">justTrimmedNames</span><span class="p">;</span></span>
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1012
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1012
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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">justScrappedNames</span><span class="p">;</span></span>
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1013
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">iterator</span> <span class="n" style="color: #333;">itCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameCount</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">itCount</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nameCount</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">++</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="1015" 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="1015" 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">@@ -1015,25 +1015,42 @@ int TrimSeqsCommand::processNamesCountFiles(string trimFasta, set<string> badNam</td>
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1015
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1015
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">justScrappedNames</span><span class="p">[</span><span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span> <span class="p">}</span></span>
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1016
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1016
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<pre style="margin: 0;"> <span id="LC1016" class="line" lang="cpp"> <span class="p">}</span></span>
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1017
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1017
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<pre style="margin: 0;"> <span id="LC1017" class="line" lang="cpp"> </span>
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1018
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<pre style="margin: 0;">-<span id="LC1018" class="line" lang="cpp"> <span class="n" style="color: #333;">CountTable</span> <span class="n" style="color: #333;">newCt</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//trimmed file</span></span>
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1019
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<pre style="margin: 0;">-<span id="LC1019" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">iterator</span> <span class="n" style="color: #333;">itCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">itCount</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">newCt</span><span class="p">.</span><span class="n" style="color: #333;">addGroup</span><span class="p">(</span><span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">);</span> <span class="p">}</span></span>
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1020
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<pre style="margin: 0;">-<span id="LC1020" 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;">tempCounts</span><span class="p">;</span> <span class="n" style="color: #333;">tempCounts</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1021
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<pre style="margin: 0;">-<span id="LC1021" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">iterator</span> <span class="n" style="color: #333;">itNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">justTrimmedNames</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">itNames</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">justTrimmedNames</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1022" class="line" lang="cpp"> <span class="n" style="color: #333;">newCt</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">tempCounts</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//add it to the table with no abundance so we can set the groups abundance</span></span>
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<pre style="margin: 0;">-<span id="LC1023" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groupMap</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>
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1024
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<pre style="margin: 0;">-<span id="LC1024" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">groupMap</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span> <span class="n" style="color: #333;">newCt</span><span class="p">.</span><span class="n" style="color: #333;">setAbund</span><span class="p">(</span><span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">it2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span> <span class="p">}</span></span>
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1025
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<td class="diff-line-num new_line old" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1025" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"[ERROR]: missing group info for "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</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 class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setControl_pressed</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="p">}</span></span>
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1026
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<td class="diff-line-num new_line old" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1026" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1027
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<td class="diff-line-num new_line old" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1027" class="line" lang="cpp"> <span class="n" style="color: #333;">newCt</span><span class="p">.</span><span class="n" style="color: #333;">printTable</span><span class="p">(</span><span class="n" style="color: #333;">trimCountFileName</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1028
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<td class="diff-line-num new_line old" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1028" class="line" lang="cpp"> </span>
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1029
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<td class="diff-line-num new_line old" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1029" class="line" lang="cpp"> <span class="n" style="color: #333;">CountTable</span> <span class="n" style="color: #333;">newScrapCt</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//scrap file</span></span>
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1030
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<td class="diff-line-num new_line old" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1030" class="line" lang="cpp"> <span class="n" style="color: #333;">newScrapCt</span><span class="p">.</span><span class="n" style="color: #333;">addGroup</span><span class="p">(</span><span class="s" style="color: #d14;">"scrap"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1031
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<td class="diff-line-num new_line old" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1031" 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;">myCounts</span><span class="p">;</span> <span class="n" style="color: #333;">tempCounts</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1032
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<td class="diff-line-num new_line old" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1032" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">iterator</span> <span class="n" style="color: #333;">itNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">justScrappedNames</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">itNames</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">justScrappedNames</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1033
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<td class="diff-line-num new_line old" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1033" class="line" lang="cpp"> <span class="n" style="color: #333;">newScrapCt</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">myCounts</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//add it to the table with no abundance so we can set the groups abundance</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1034
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<td class="diff-line-num new_line old" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1034" class="line" lang="cpp"> <span class="n" style="color: #333;">newScrapCt</span><span class="p">.</span><span class="n" style="color: #333;">setAbund</span><span class="p">(</span><span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="s" style="color: #d14;">"scrap"</span><span class="p">,</span> <span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//create a count table with group info</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">groupCounts</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;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">groupCounts</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;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1022" 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">
1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="cpp"> <span class="n" style="color: #333;">CountTable</span> <span class="n" style="color: #333;">newCt</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//trimmed file</span></span>
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1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">iterator</span> <span class="n" style="color: #333;">itCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">itCount</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">newCt</span><span class="p">.</span><span class="n" style="color: #333;">addGroup</span><span class="p">(</span><span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">);</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1024" 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">
1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1025" 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">
1025
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<pre style="margin: 0;">+<span id="LC1025" 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;">tempCounts</span><span class="p">;</span> <span class="n" style="color: #333;">tempCounts</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">groupCounts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1026" 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">
1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">iterator</span> <span class="n" style="color: #333;">itNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">justTrimmedNames</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">itNames</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">justTrimmedNames</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1027" 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">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="cpp"> <span class="n" style="color: #333;">newCt</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">tempCounts</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//add it to the table with no abundance so we can set the groups abundance</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1028" 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">
1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groupMap</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1029" 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">
1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">groupMap</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span> <span class="n" style="color: #333;">newCt</span><span class="p">.</span><span class="n" style="color: #333;">setAbund</span><span class="p">(</span><span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">it2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1030" 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">
1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"[ERROR]: missing group info for "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</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 class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setControl_pressed</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1031" 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">
1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1032" 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">
1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="cpp"> <span class="n" style="color: #333;">newCt</span><span class="p">.</span><span class="n" style="color: #333;">printTable</span><span class="p">(</span><span class="n" style="color: #333;">trimCountFileName</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1033" 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">
1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1034" 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">
1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="cpp"> <span class="n" style="color: #333;">CountTable</span> <span class="n" style="color: #333;">newScrapCt</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//scrap file</span></span>
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1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="cpp"> <span class="n" style="color: #333;">newScrapCt</span><span class="p">.</span><span class="n" style="color: #333;">addGroup</span><span class="p">(</span><span class="s" style="color: #d14;">"scrap"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1036" 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">
1036
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<pre style="margin: 0;">+<span id="LC1036" 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;">myCounts</span><span class="p">;</span> <span class="n" style="color: #333;">tempCounts</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1037" 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">
1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">iterator</span> <span class="n" style="color: #333;">itNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">justScrappedNames</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">itNames</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">justScrappedNames</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1038" 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">
1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="cpp"> <span class="n" style="color: #333;">newScrapCt</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">myCounts</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//add it to the table with no abundance so we can set the groups abundance</span></span>
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1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="cpp"> <span class="n" style="color: #333;">newScrapCt</span><span class="p">.</span><span class="n" style="color: #333;">setAbund</span><span class="p">(</span><span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="s" style="color: #d14;">"scrap"</span><span class="p">,</span> <span class="n" style="color: #333;">itNames</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="cpp"> <span class="p">}</span></span>
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1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="cpp"> <span class="n" style="color: #333;">newScrapCt</span><span class="p">.</span><span class="n" style="color: #333;">printTable</span><span class="p">(</span><span class="n" style="color: #333;">scrapCountFileName</span><span class="p">);</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1043" 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">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//create a count file without groups</span></span>
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1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="cpp"> <span class="n" style="color: #333;">CountTable</span> <span class="n" style="color: #333;">newCt</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//trimmed file</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1045" 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">
1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="cpp"> <span class="n" style="color: #333;">CountTable</span> <span class="n" style="color: #333;">newScrapCt</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//scrap file</span></span>
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1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1047" 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">
1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">iterator</span> <span class="n" style="color: #333;">itCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameCount</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">itCount</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nameCount</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1048" 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">
1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">badNames</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">newCt</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span> <span class="p">}</span></span>
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1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">newScrapCt</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">itCount</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span> <span class="p">}</span></span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="cpp"> <span class="p">}</span></span>
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1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="cpp"> <span class="n" style="color: #333;">newCt</span><span class="p">.</span><span class="n" style="color: #333;">printTable</span><span class="p">(</span><span class="n" style="color: #333;">trimCountFileName</span><span class="p">);</span></span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="cpp"> <span class="n" style="color: #333;">newScrapCt</span><span class="p">.</span><span class="n" style="color: #333;">printTable</span><span class="p">(</span><span class="n" style="color: #333;">scrapCountFileName</span><span class="p">);</span></span>
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1035
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1053
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<pre style="margin: 0;"> <span id="LC1053" class="line" lang="cpp"> <span class="p">}</span></span>
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1036
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<pre style="margin: 0;">-<span id="LC1036" class="line" lang="cpp"> <span class="n" style="color: #333;">newScrapCt</span><span class="p">.</span><span class="n" style="color: #333;">printTable</span><span class="p">(</span><span class="n" style="color: #333;">scrapCountFileName</span><span class="p">);</span></span>
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1037
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1054
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<pre style="margin: 0;"> <span id="LC1054" class="line" lang="cpp"> <span class="p">}</span></span>
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1038
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1055
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="cpp"></span>
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1039
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1056
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">allFiles</span><span class="p">){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1084" 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">@@ -1067,38 +1084,38 @@ int TrimSeqsCommand::processNamesCountFiles(string trimFasta, set<string> badNam</td>
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1067
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1084
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<pre style="margin: 0;"> <span id="LC1084" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**************************************************************************************************/</span></span>
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1068
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1085
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<pre style="margin: 0;"> <span id="LC1085" class="line" lang="cpp"></span>
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1069
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<td class="diff-line-num new_line" data-linenumber="1086" 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">
1086
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<pre style="margin: 0;"> <span id="LC1086" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">TrimSeqsCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setLines</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">qfilename</span><span class="p">)</span> <span class="p">{</span></span>
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1070
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<td class="diff-line-num new_line old" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1070" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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1071
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<td class="diff-line-num new_line" data-linenumber="1088" 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">
1088
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<pre style="margin: 0;"> <span id="LC1088" class="line" lang="cpp"> </span>
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1072
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<td class="diff-line-num new_line" data-linenumber="1089" 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">
1089
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<pre style="margin: 0;"> <span id="LC1089" 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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fastaFilePos</span><span class="p">;</span></span>
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1073
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<td class="diff-line-num new_line old" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1073" class="line" lang="cpp"><span class="idiff left right"> </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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">qfileFilePos</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1074
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<pre style="margin: 0;">-<span id="LC1074" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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1075
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<pre style="margin: 0;">-<span id="LC1075" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#if defined NON_WINDOWS</span></span>
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1076
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<pre style="margin: 0;">-<span id="LC1076" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//set file positions for fasta file</span></span>
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1077
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<pre style="margin: 0;">-<span id="LC1077" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">fastaFilePos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">divideFile</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">processors</span><span class="p">);</span></span>
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1078
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<pre style="margin: 0;">-<span id="LC1078" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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1079
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<pre style="margin: 0;">-<span id="LC1079" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//get name of first sequence in each chunk</span></span>
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1080
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<pre style="margin: 0;">-<span id="LC1080" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">firstSeqNames</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1081
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<pre style="margin: 0;">-<span id="LC1081" class="line" lang="cpp"><span class="idiff left right"> </span><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="p">(</span><span class="n" style="color: #333;">fastaFilePos</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;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1082
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<pre style="margin: 0;">-<span id="LC1082" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">in</span><span class="p">;</span></span>
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1083
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<pre style="margin: 0;">-<span id="LC1083" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">openInputFile</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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1084
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<td class="diff-line-num new_line old" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1084" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">seekg</span><span class="p">(</span><span class="n" style="color: #333;">fastaFilePos</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="cpp"><span class="idiff left right"> </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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">qfileFilePos</span><span class="p">;</span></span>
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1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#if defined NON_WINDOWS</span></span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//set file positions for fasta file</span></span>
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1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">fastaFilePos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">divideFile</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">processors</span><span class="p">);</span></span>
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1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="cpp"><span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">//get name of first sequence in each chunk</span></span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">firstSeqNames</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1098" 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">
1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="cpp"><span class="idiff left right"> </span><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="p">(</span><span class="n" style="color: #333;">fastaFilePos</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;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1099" 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">
1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">in</span><span class="p">;</span></span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">openInputFile</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">seekg</span><span class="p">(</span><span class="n" style="color: #333;">fastaFilePos</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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1085
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1102
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<pre style="margin: 0;"> <span id="LC1102" class="line" lang="cpp"> </span>
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1086
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1103
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<pre style="margin: 0;"> <span id="LC1103" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//adjust start if null strings</span></span>
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1087
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1104
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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">zapGremlins</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">);</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">gobble</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">);</span> <span class="p">}</span></span>
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1088
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<pre style="margin: 0;">-<span id="LC1088" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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1089
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<pre style="margin: 0;">-<span id="LC1089" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Sequence</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">in</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span></span>
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1090
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<pre style="margin: 0;">-<span id="LC1090" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">firstSeqNames</span><span class="p">[</span><span class="n" style="color: #333;">temp</span><span class="p">.</span><span class="n" style="color: #333;">getName</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>
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1091
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<pre style="margin: 0;">-<span id="LC1091" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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1092
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<pre style="margin: 0;">-<span id="LC1092" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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1093
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<pre style="margin: 0;">-<span id="LC1093" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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1094
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<td class="diff-line-num new_line 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: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1094" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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1095
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<td class="diff-line-num new_line 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: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1095" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">qfilename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Sequence</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">temp</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">in</span></span><span class="p"><span class="idiff right">);</span></span></span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">firstSeqNames</span><span class="p">[</span><span class="n" style="color: #333;">temp</span><span class="p">.</span><span class="n" style="color: #333;">getName</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>
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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1110" 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">
1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">qfilename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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1096
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1113
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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//seach for filePos of each first name in the qfile and save in qfileFilePos</span></span>
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1097
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1114
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<pre style="margin: 0;"> <span id="LC1114" class="line" lang="cpp"> <span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">inQual</span><span class="p">;</span></span>
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1098
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1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="cpp"> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">openInputFile</span><span class="p">(</span><span class="n" style="color: #333;">qfilename</span><span class="p">,</span> <span class="n" style="color: #333;">inQual</span><span class="p">);</span></span>
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1099
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="cpp"> </span>
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1100
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1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">input</span><span class="p">;</span></span>
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1101
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<pre style="margin: 0;">-<span id="LC1101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">inQual</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">()){</span><span class="idiff left right"> </span></span>
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1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">inQual</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">()){</span></span>
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1102
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<td class="diff-line-num new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
1119
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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="cpp"> <span class="n" style="color: #333;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">inQual</span><span class="p">);</span></span>
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1103
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1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="cpp"> </span>
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1104
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1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">input</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="mi" style="color: #099;">0</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="1114" 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="1131" 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">@@ -1114,7 +1131,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {</td>
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1114
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1131
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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="cpp"> </span>
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1115
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1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">firstSeqNames</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//this is the start of a new chunk</span></span>
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1116
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1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inQual</span><span class="p">.</span><span class="n" style="color: #333;">tellg</span><span class="p">();</span></span>
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1117
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<pre style="margin: 0;">-<span id="LC1117" class="line" lang="cpp"> <span class="n" style="color: #333;">qfileFilePos</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">input</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="mi" style="color: #099;">1</span><span class="p">);</span><span class="idiff left right"> </span></span>
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1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="cpp"> <span class="n" style="color: #333;">qfileFilePos</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">input</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="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1118
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1135
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="cpp"> <span class="n" style="color: #333;">firstSeqNames</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>
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1119
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1136
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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="cpp"> <span class="p">}</span></span>
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1120
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1137
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<pre style="margin: 0;"> <span id="LC1137" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1125" 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="1142" 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">@@ -1125,9 +1142,9 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {</td>
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1125
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1142
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="cpp"> <span class="n" style="color: #333;">inQual</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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1126
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1143
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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp"> </span>
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1127
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1144
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="cpp"> </span>
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1128
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<pre style="margin: 0;">-<span id="LC1128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstSeqNames</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;">0</span><span class="p">)</span> <span class="p">{</span><span class="idiff left right"> </span></span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstSeqNames</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;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1129
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<td class="diff-line-num new_line" data-linenumber="1146" 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">
1146
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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">firstSeqNames</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">firstSeqNames</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1130
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<td class="diff-line-num new_line old" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1130" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" is in your fasta file and not in your quality file, not using quality file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span><span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1147" 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">
1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" is in your fasta file and not in your quality file, not using quality file.</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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1131
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1148
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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="cpp"> <span class="p">}</span></span>
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1132
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<td class="diff-line-num new_line" data-linenumber="1149" 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">
1149
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<pre style="margin: 0;"> <span id="LC1149" class="line" lang="cpp"> <span class="n" style="color: #333;">qFileName</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1133" 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">
1133
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1150
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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">processors</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1169" 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">@@ -1152,25 +1169,25 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {</td>
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1152
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1169
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<pre style="margin: 0;"> <span id="LC1169" class="line" lang="cpp"> </span>
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1153
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<td class="diff-line-num new_line" data-linenumber="1170" 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">
1170
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<pre style="margin: 0;"> <span id="LC1170" 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="p">(</span><span class="n" style="color: #333;">fastaFilePos</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;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1154
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<td class="diff-line-num new_line" data-linenumber="1171" 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">
1171
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<pre style="margin: 0;"> <span id="LC1171" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDebug</span><span class="p">())</span> <span class="p">{</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"[DEBUG]: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</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="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">fastaFilePos</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="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">fastaFilePos</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span> <span class="p">}</span></span>
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1155
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<td class="diff-line-num new_line old" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1155" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">linePair</span><span class="p">(</span><span class="n" style="color: #333;">fastaFilePos</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">fastaFilePos</span><span class="p">[(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)]));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1156
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<td class="diff-line-num new_line old" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1156" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qfilename</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">qLines</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">linePair</span><span class="p">(</span><span class="n" style="color: #333;">qfileFilePos</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">qfileFilePos</span><span class="p">[(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)]));</span> <span class="p">}</span></span>
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1157
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<td class="diff-line-num new_line old" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1157" class="line" lang="cpp"><span class="idiff left"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff right"> </span></span>
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<td class="diff-line-num old old_line" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1158
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<td class="diff-line-num new_line old" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1158" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">qfilename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qLines</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lines</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//files with duds</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1159
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<td class="diff-line-num new_line old" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1159" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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1160
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<td class="diff-line-num new_line old" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1160" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">processors</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1161
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<td class="diff-line-num new_line old" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1161" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num old old_line" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1162
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<td class="diff-line-num new_line old" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1162" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1163" 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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1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">linePair</span><span class="p">(</span><span class="n" style="color: #333;">fastaFilePos</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">fastaFilePos</span><span class="p">[(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)]));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1173" 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">
1173
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<pre style="margin: 0;">+<span id="LC1173" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qfilename</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">qLines</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">linePair</span><span class="p">(</span><span class="n" style="color: #333;">qfileFilePos</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">qfileFilePos</span><span class="p">[(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)]));</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1174" 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">
1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="cpp"><span class="idiff left"> </span><span class="p"><span class="idiff right">}</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1175" 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">
1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">qfilename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qLines</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lines</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//files with duds</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1176" 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">
1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="1177" 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">
1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">processors</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1178" 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">
1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="1179" 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">
1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1163
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1180
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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="cpp"> </span>
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1164
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1181
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<pre style="margin: 0;"> <span id="LC1181" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">numFastaSeqs</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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1165
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<pre style="margin: 0;">-<span id="LC1165" class="line" lang="cpp"> <span class="n" style="color: #333;">fastaFilePos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">setFilePosFasta</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">numFastaSeqs</span><span class="p">);</span><span class="idiff left right"> </span></span>
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1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="cpp"> <span class="n" style="color: #333;">fastaFilePos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">setFilePosFasta</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">numFastaSeqs</span><span class="p">);</span></span>
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1166
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<td class="diff-line-num new_line" data-linenumber="1183" 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">
1183
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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numFastaSeqs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">processors</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">processors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numFastaSeqs</span><span class="p">;</span> <span class="p">}</span></span>
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1167
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1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="cpp"> </span>
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1168
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<pre style="margin: 0;">-<span id="LC1168" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qfilename</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span><span class="idiff left right"> </span></span>
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1185
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qfilename</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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1169
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1186
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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">numQualSeqs</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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1170
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<pre style="margin: 0;">-<span id="LC1170" class="line" lang="cpp"> <span class="n" style="color: #333;">qfileFilePos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">setFilePosFasta</span><span class="p">(</span><span class="n" style="color: #333;">qfilename</span><span class="p">,</span> <span class="n" style="color: #333;">numQualSeqs</span><span class="p">);</span><span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="1171" 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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1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="cpp"> <span class="n" style="color: #333;">qfileFilePos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">setFilePosFasta</span><span class="p">(</span><span class="n" style="color: #333;">qfilename</span><span class="p">,</span> <span class="n" style="color: #333;">numQualSeqs</span><span class="p">);</span></span>
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1171
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1188
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<pre style="margin: 0;"> <span id="LC1188" class="line" lang="cpp"> </span>
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1172
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1189
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<pre style="margin: 0;"> <span id="LC1189" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numFastaSeqs</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">numQualSeqs</span><span class="p">)</span> <span class="p">{</span></span>
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1173
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<td class="diff-line-num new_line old" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1173" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"[ERROR]: You have "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">numFastaSeqs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" sequences in your fasta file, but "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">numQualSeqs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" sequences in your quality file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setControl_pressed</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span><span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="1174" 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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1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mothurOut</span><span class="p">(</span><span class="s" style="color: #d14;">"[ERROR]: You have "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">numFastaSeqs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" sequences in your fasta file, but "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">numQualSeqs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" sequences in your quality file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setControl_pressed</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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1174
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1191
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<pre style="margin: 0;"> <span id="LC1191" class="line" lang="cpp"> <span class="p">}</span></span>
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1175
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1192
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<pre style="margin: 0;"> <span id="LC1192" class="line" lang="cpp"> <span class="p">}</span></span>
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1176
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1193
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<pre style="margin: 0;"> <span id="LC1193" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1178" 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="1195" 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">@@ -1178,20 +1195,20 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {</td>
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1178
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1195
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<pre style="margin: 0;"> <span id="LC1195" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numSeqsPerProcessor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numFastaSeqs</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">processors</span><span class="p">;</span></span>
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1179
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1196
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<pre style="margin: 0;"> <span id="LC1196" 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;">processors</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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<td class="diff-line-num old_line" data-linenumber="1180" 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">
1180
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<td class="diff-line-num new_line" data-linenumber="1197" 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">
1197
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<pre style="margin: 0;"> <span id="LC1197" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">startIndex</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="n" style="color: #333;">numSeqsPerProcessor</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1181
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<td class="diff-line-num new_line old" data-linenumber="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">processors</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)){</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">numSeqsPerProcessor</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numFastaSeqs</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numSeqsPerProcessor</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1198" 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">
1198
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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">processors</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)){</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">numSeqsPerProcessor</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numFastaSeqs</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numSeqsPerProcessor</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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1182
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<td class="diff-line-num new_line" data-linenumber="1199" 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">
1199
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<pre style="margin: 0;"> <span id="LC1199" class="line" lang="cpp"> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">linePair</span><span class="p">(</span><span class="n" style="color: #333;">fastaFilePos</span><span class="p">[</span><span class="n" style="color: #333;">startIndex</span><span class="p">],</span> <span class="n" style="color: #333;">numSeqsPerProcessor</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="1183" 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">
1183
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<td class="diff-line-num new_line" data-linenumber="1200" 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">
1200
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<pre style="margin: 0;"> <span id="LC1200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qfilename</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">qLines</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">linePair</span><span class="p">(</span><span class="n" style="color: #333;">qfileFilePos</span><span class="p">[</span><span class="n" style="color: #333;">startIndex</span><span class="p">],</span> <span class="n" style="color: #333;">numSeqsPerProcessor</span><span class="p">));</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1184" 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">
1184
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<td class="diff-line-num new_line" data-linenumber="1201" 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">
1201
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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1185" 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">
1185
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<td class="diff-line-num new_line" data-linenumber="1202" 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">
1202
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="cpp"> </span>
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<td class="diff-line-num old old_line" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1186
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<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1186" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qfilename</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qLines</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lines</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//files with duds</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1187
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<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1187" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1188
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<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1188" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num old old_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1189
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<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1189" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1190
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<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1190" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1191
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<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1191" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1192
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<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1192" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"setLines"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1193
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<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1193" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1194
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<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1194" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1203" 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">
1203
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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qfilename</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qLines</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lines</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//files with duds</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1204" 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">
1204
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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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1206
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<pre style="margin: 0;">+<span id="LC1206" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1209" 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">
1209
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorOut</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"TrimSeqsCommand"</span><span class="p">,</span> <span class="s" style="color: #d14;">"setLines"</span><span class="p">);</span></span>
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1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1211
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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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1195
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1212
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<pre style="margin: 0;"> <span id="LC1212" class="line" lang="cpp"><span class="p">}</span></span>
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1196
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1213
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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//***************************************************************************************************************</span></span>
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1197
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1214
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<pre style="margin: 0;"> <span id="LC1214" class="line" lang="cpp"></span></pre>
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<a href="https://salsa.debian.org/med-team/mothur/-/compare/3fb847522be597c27070057314421a173fc780f8...79abd0c5b1995dd2ce822c77e80d7fa6b18f8456#4356bb76a146ce04fb34b84f985b7c6d5e5c2c71"><strong>source/commands/trimseqscommand.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">@@ -23,43 +23,42 @@</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TrimSeqsCommand</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Command</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="nl">public:</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">TrimSeqsCommand</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"><span class="idiff left right"> </span><span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">TrimSeqsCommand</span><span class="p">(){}</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">vector</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;">setParameters</span><span class="p">();</span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">getCommandName</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"trim.seqs"</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">getCommandCategory</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"Sequence Processing"</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">getHelpString</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getOutputPattern</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">);</span><span class="idiff left right"> </span></span>
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<td class="diff-line-num new_line old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getCitation</span><span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"http://www.mothur.org/wiki/Trim.seqs"</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new_line old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">getDescription</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff right"> </span><span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"provides the preprocessing features needed to screen and sort pyrosequences"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">TrimSeqsCommand</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="idiff left right"> </span><span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">TrimSeqsCommand</span><span class="p">(){}</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">vector</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;">setParameters</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">getCommandName</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"trim.seqs"</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">getCommandCategory</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"Sequence Processing"</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">getHelpString</span></span><span class="p"><span class="idiff right">();</span></span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getOutputPattern</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getCitation</span><span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"http://www.mothur.org/wiki/Trim.seqs"</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" 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">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">getDescription</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff right"> </span><span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"provides the preprocessing features needed to screen and sort pyrosequences"</span><span class="p">;</span> <span class="p">}</span></span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"><span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">execute</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"><span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">help</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOut</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">getHelpString</span></span><span class="p"><span class="idiff">());</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"><span class="nl">private:</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">abort</span><span class="p">,</span> <span class="n" style="color: #333;">createGroup</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fastaFile</span><span class="p">,</span> <span class="n" style="color: #333;">oligoFile</span><span class="p">,</span> <span class="n" style="color: #333;">qFileName</span><span class="p">,</span> <span class="n" style="color: #333;">groupfile</span><span class="p">,</span> <span class="n" style="color: #333;">nameFile</span><span class="p">,</span> <span class="n" style="color: #333;">countfile</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">flip</span><span class="p">,</span> <span class="n" style="color: #333;">allFiles</span><span class="p">,</span> <span class="n" style="color: #333;">qtrim</span><span class="p">,</span> <span class="n" style="color: #333;">keepforward</span><span class="p">,</span> <span class="n" style="color: #333;">pairedOligos</span><span class="p">,</span> <span class="n" style="color: #333;">reorient</span><span class="p">,</span> <span class="n" style="color: #333;">logtransform</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxAmbig</span><span class="p">,</span> <span class="n" style="color: #333;">maxHomoP</span><span class="p">,</span> <span class="n" style="color: #333;">minLength</span><span class="p">,</span> <span class="n" style="color: #333;">maxLength</span><span class="p">,</span> <span class="n" style="color: #333;">processors</span><span class="p">,</span> <span class="n" style="color: #333;">tdiffs</span><span class="p">,</span> <span class="n" style="color: #333;">bdiffs</span><span class="p">,</span> <span class="n" style="color: #333;">pdiffs</span><span class="p">,</span> <span class="n" style="color: #333;">ldiffs</span><span class="p">,</span> <span class="n" style="color: #333;">sdiffs</span><span class="p">,</span> <span class="n" style="color: #333;">comboStarts</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qWindowSize</span><span class="p">,</span> <span class="n" style="color: #333;">qWindowStep</span><span class="p">,</span> <span class="n" style="color: #333;">keepFirst</span><span class="p">,</span> <span class="n" style="color: #333;">removeLast</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">qRollAverage</span><span class="p">,</span> <span class="n" style="color: #333;">qThreshold</span><span class="p">,</span> <span class="n" style="color: #333;">qWindowAverage</span><span class="p">,</span> <span class="n" style="color: #333;">qAverage</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">vector</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;">outputNames</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">set</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;">filesToRemove</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">vector</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;">groupVector</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">map</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">groupCounts</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nameMap</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"><span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">execute</span></span><span class="p"><span class="idiff right">();</span></span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"><span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">help</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">mothurOut</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">getHelpString</span></span><span class="p"><span class="idiff">());</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">}</span></span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"><span class="nl">private:</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">abort</span><span class="p">,</span> <span class="n" style="color: #333;">createGroup</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fastaFile</span><span class="p">,</span> <span class="n" style="color: #333;">oligoFile</span><span class="p">,</span> <span class="n" style="color: #333;">qFileName</span><span class="p">,</span> <span class="n" style="color: #333;">groupfile</span><span class="p">,</span> <span class="n" style="color: #333;">nameFile</span><span class="p">,</span> <span class="n" style="color: #333;">countfile</span><span class="p">;</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">flip</span><span class="p">,</span> <span class="n" style="color: #333;">allFiles</span><span class="p">,</span> <span class="n" style="color: #333;">qtrim</span><span class="p">,</span> <span class="n" style="color: #333;">keepforward</span><span class="p">,</span> <span class="n" style="color: #333;">pairedOligos</span><span class="p">,</span> <span class="n" style="color: #333;">reorient</span><span class="p">,</span> <span class="n" style="color: #333;">logtransform</span><span class="p">;</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxAmbig</span><span class="p">,</span> <span class="n" style="color: #333;">maxHomoP</span><span class="p">,</span> <span class="n" style="color: #333;">minLength</span><span class="p">,</span> <span class="n" style="color: #333;">maxLength</span><span class="p">,</span> <span class="n" style="color: #333;">processors</span><span class="p">,</span> <span class="n" style="color: #333;">tdiffs</span><span class="p">,</span> <span class="n" style="color: #333;">bdiffs</span><span class="p">,</span> <span class="n" style="color: #333;">pdiffs</span><span class="p">,</span> <span class="n" style="color: #333;">ldiffs</span><span class="p">,</span> <span class="n" style="color: #333;">sdiffs</span><span class="p">,</span> <span class="n" style="color: #333;">comboStarts</span><span class="p">;</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qWindowSize</span><span class="p">,</span> <span class="n" style="color: #333;">qWindowStep</span><span class="p">,</span> <span class="n" style="color: #333;">keepFirst</span><span class="p">,</span> <span class="n" style="color: #333;">removeLast</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">qRollAverage</span><span class="p">,</span> <span class="n" style="color: #333;">qThreshold</span><span class="p">,</span> <span class="n" style="color: #333;">qWindowAverage</span><span class="p">,</span> <span class="n" style="color: #333;">qAverage</span><span class="p">;</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">vector</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;">outputNames</span><span class="p">;</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">set</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;">filesToRemove</span><span class="p">;</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">vector</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;">groupVector</span><span class="p">;</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">map</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">groupCounts</span></span><span class="p"><span class="idiff right">;</span></span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nameMap</span><span class="p">;</span></span>
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54
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</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;">nameCount</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//for countfile name -> repCount</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">groupMap</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//for countfile name -> group</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"></span>
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<td class="diff-line-num new_line old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">linePair</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lines</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">linePair</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">qLines</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new_line old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">createProcessesCreateTrim</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">);</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">linePair</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lines</span><span class="p">;</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">linePair</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">qLines</span><span class="p">;</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">createProcessesCreateTrim</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">processNamesCountFiles</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimFasta</span><span class="p">,</span> <span class="n" style="color: #333;">set</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;">badNames</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">groupMap</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimNameFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapNameFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimCountFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scrapCountFileName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">groupFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">setLines</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">setLines</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**************************************************************************************************/</span></span>
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