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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/sniffles">Debian Med / sniffles</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sniffles/commit/4cb082cc94b887ca4a4226c7af22a26b3e5f5302">4cb082cc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-02-01T14:28:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.11+ds</pre>
</li>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#079f6c72660dd1efe75df479ad20713bcb2cb722">
src/Alignment.cpp
</a>
</li>
<li class="file-stats">
<a href="#46a0eac0df27bbdf49c8effa7531b4766967e289">
src/Paramer.h
</a>
</li>
<li class="file-stats">
<a href="#c758ea5b1649f4f7b6c0f8ba9660a877a95487e0">
src/Sniffles.cpp
</a>
</li>
<li class="file-stats">
<a href="#6559993eb064f711fc203323d78ac236f9ab998b">
src/print/VCFPrinter.cpp
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/sniffles/commit/4cb082cc94b887ca4a4226c7af22a26b3e5f5302#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" 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">@@ -7,9 +7,9 @@ option(STATIC "Build static binary" OFF)</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SNIF_VERSION_MINOR 0 <span class="p">)</span></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">IF</span><span class="p">(</span>CMAKE_BUILD_TYPE STREQUAL <span class="s2" style="color: #d14;">"Debug"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">message</span><span class="p">(</span>STATUS <span class="s2" style="color: #d14;">"Building in debug mode!"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SNIF_VERSION_BUILD 1<span class="idiff left right">0</span>-debug <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SNIF_VERSION_BUILD 1<span class="idiff left right">1</span>-debug <span class="p">)</span></span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SNIF_VERSION_BUILD 1<span class="idiff left right">0</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SNIF_VERSION_BUILD 1<span class="idiff left right">1</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ENDIF</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"></span>
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<li id="079f6c72660dd1efe75df479ad20713bcb2cb722">
<a href="https://salsa.debian.org/med-team/sniffles/commit/4cb082cc94b887ca4a4226c7af22a26b3e5f5302#079f6c72660dd1efe75df479ad20713bcb2cb722"><strong>src/Alignment.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" 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="61" 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">@@ -61,6 +61,7 @@ void add_event(int pos, size_t & i, vector<differences_str> & events) {</td>
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<pre style="margin: 0;"> <span id="LC61" 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="LC62" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC63" 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;">differences_str</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">summarize_csstring</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">indel_str</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dels</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cs</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_cs</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getPosition</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">corr</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -137,8 +138,11 @@ vector<differences_str> Alignment::summarizeAlignment(std::vector<indel_str> &de</td>
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137
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">Length</span><span class="p">;</span></span>
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138
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="p">}</span></span>
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139
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sum_mis</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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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sum_events</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="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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sum_single</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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140
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144
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<pre style="margin: 0;"> <span id="LC144" 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;">size_t</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;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">)</span> <span class="p">{</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'M'</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">al</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">CigarData</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">Type</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">'='</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">al</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">CigarData</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">Type</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">'X'</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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142
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Length</span><span class="p">;</span></span>
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143
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Length</span><span class="p">;</span></span>
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144
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="p">}</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;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'D'</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">@@ -146,6 +150,11 @@ vector<differences_str> Alignment::summarizeAlignment(std::vector<indel_str> &de</td>
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146
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">ev</span><span class="p">.</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Length</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//deletion</span></span>
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147
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">ev</span><span class="p">.</span><span class="n" style="color: #333;">readposition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_pos</span><span class="p">;</span></span>
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148
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">ev</span><span class="p">.</span><span class="n" style="color: #333;">resolved</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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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Length</span> <span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_events</span><span class="o" style="font-weight: 600;">++</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="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_single</span><span class="o" style="font-weight: 600;">++</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="p">}</span></span>
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149
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">events</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ev</span><span class="p">);</span></span>
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150
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Length</span><span class="p">;</span></span>
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151
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"> <span class="p">}</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;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="162" 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">@@ -153,13 +162,19 @@ vector<differences_str> Alignment::summarizeAlignment(std::vector<indel_str> &de</td>
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153
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">ev</span><span class="p">.</span><span class="n" style="color: #333;">resolved</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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154
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">ev</span><span class="p">.</span><span class="n" style="color: #333;">readposition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_pos</span><span class="p">;</span></span>
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155
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">ev</span><span class="p">.</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Length</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="c1" style="color: #998; font-style: italic;">//insertion</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Length</span> <span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_events</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" 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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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_single</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="p">}</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"></span>
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156
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">events</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ev</span><span class="p">);</span></span>
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157
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Length</span><span class="p">;</span></span>
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158
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="p">}</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;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Type</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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159
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Length</span><span class="p">;</span></span>
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160
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<td class="diff-line-num new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;">ev</span><span class="p">.</span><span class="n" style="color: #333;">resolved</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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<td class="diff-line-num old_line" data-linenumber="161" 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">
161
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<td class="diff-line-num new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">Length</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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<td class="diff-line-num new_line old" data-linenumber="177" 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="LC162" class="line" lang="cpp"> <span class="p">}</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;"><span class="idiff left">al</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">CigarData</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">Type</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="idiff right"> </span><span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">huge_ins</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">/// Used for reads ranging into an inser</span></span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">al</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">CigarData</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">Type</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="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">al</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">CigarData</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">Type</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="idiff"> </span><span class="p"><span class="idiff right">)</span></span><span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CigarData</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">huge_ins</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">/// Used for reads ranging into an inser</span></span>
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163
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sa</span><span class="p">;</span></span>
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164
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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;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetTag</span><span class="p">(</span><span class="s" style="color: #d14;">"SA"</span><span class="p">,</span> <span class="n" style="color: #333;">sa</span><span class="p">);</span></span>
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165
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sv</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="232" 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">@@ -217,6 +232,7 @@ vector<differences_str> Alignment::summarizeAlignment(std::vector<indel_str> &de</td>
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217
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="p">}</span></span>
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218
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"> <span class="n" style="color: #333;">ref_pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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219
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"> <span class="p">}</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_mis</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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220
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//store in sorted order:</span></span>
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221
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">add_event</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">pos_events</span><span class="p">,</span> <span class="n" style="color: #333;">events</span><span class="p">);</span></span>
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222
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//just the pos on ref!</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="256" 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">@@ -240,6 +256,12 @@ vector<differences_str> Alignment::summarizeAlignment(std::vector<indel_str> &de</td>
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240
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="p">}</span></span>
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241
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"> <span class="p">}</span></span>
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242
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (flag) {</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// std::cout << this->getName() << " " << (double) sum_mis << " " << (double) sum_events<<" "<<sum_single <<" "<< (double) sum_mis / (double) (sum_single+sum_mis)<< endl;</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (Parameter::Instance()->ccs_reads && (double) sum_mis / (double) (sum_events+sum_mis) > 0.95) {</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// events.clear();</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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243
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Parameter::Instance()->meassure_time(comp_aln, "\t\tMD string: ");</span></span>
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244
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"></span>
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">events</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="693" 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="715" 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">@@ -693,7 +715,7 @@ vector<aln_str> Alignment::getSA(RefVector ref) {</td>
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693
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715
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sv</span><span class="p">;</span></span>
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694
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">al</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetTag</span><span class="p">(</span><span class="s" style="color: #d14;">"SV"</span><span class="p">,</span> <span class="n" style="color: #333;">sv</span><span class="p">);</span></span>
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695
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717
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">cross_N</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">sv</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">Ns_CLIPPED</span><span class="p">));</span></span>
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696
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">getName</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="s" style="color: #d14;"><span class="idiff left">"0bac61ef-7819-462b-ae3d-32c68fe580c0"</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">==</span></span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Parameter::Instance()->read_name.c_str()) == 0;</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">getName</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"0bac61ef-7819-462b-ae3d-32c68fe580c0"</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 right"> </span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Parameter::Instance()->read_name.c_str()) == 0;</span></span>
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697
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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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698
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="cpp"> <span class="n" style="color: #333;">get_coords</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">read_pos_start</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">read_pos_stop</span><span class="p">);</span></span>
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699
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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">flag</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="926" 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="948" 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">@@ -926,7 +948,7 @@ std::string Alignment::get_md() {</td>
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926
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948
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<pre style="margin: 0;"> <span id="LC948" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">md</span><span class="p">;</span></span>
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927
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949
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<pre style="margin: 0;"> <span id="LC949" 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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928
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950
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<pre style="margin: 0;"> <span id="LC950" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"No MD string detected! Check bam file! Otherwise generate using e.g. samtools."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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929
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<pre style="margin: 0;">-<span id="LC929" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><span class="idiff left"><<</span></span><span class="s" style="color: #d14;"><span class="idiff">"MD: TEST"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getName</span></span><span class="p"><span class="idiff">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff right"><<</span></span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="idiff left"> </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">"MD: TEST"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getName</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 right"> </span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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930
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952
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<pre style="margin: 0;"> <span id="LC952" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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931
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953
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<pre style="margin: 0;"> <span id="LC953" class="line" lang="cpp"> <span class="p">}</span></span>
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932
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954
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">md</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1117" 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="1139" 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">@@ -1117,10 +1139,10 @@ vector<str_event> Alignment::get_events_Aln() {</td>
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1117
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1139
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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//clock_t comp_aln = clock();</span></span>
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1118
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1140
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">indel_str</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">dels</span><span class="p">;</span></span>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="1141" 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">
1141
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<pre style="margin: 0;"> <span id="LC1141" 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;">differences_str</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">event_aln</span><span class="p">;</span></span>
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1120
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<pre style="margin: 0;">-<span id="LC1120" class="line" lang="cpp"><span class="idiff left"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff right">/* if (Parameter::Instance()->cs_string) {</span></span></span>
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1121
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<pre style="margin: 0;">-<span id="LC1121" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> cout<<"run cs check "<<</span>std::endl;</span></span>
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1122
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<pre style="margin: 0;">-<span id="LC1122" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span>event_aln = summarize_csstring(dels);</span></span>
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1123
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<pre style="margin: 0;">-<span id="LC1123" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> } else {*/</span></span></span>
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1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// if (Parameter::Instance()->cs_string) {/</span></span></span>
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1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// cout << "run cs check " << </span>std::endl;</span></span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// </span>event_aln = summarize_csstring(dels);</span></span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// } else {</span></span></span>
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1124
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1146
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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="cpp"> <span class="n" style="color: #333;">event_aln</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">summarizeAlignment</span><span class="p">(</span><span class="n" style="color: #333;">dels</span><span class="p">);</span></span>
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1125
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1147
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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1126
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1148
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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//double time2 = Parameter::Instance()->meassure_time(comp_aln, "\tcompAln Events: ");</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">@@ -25,7 +25,7 @@ class Parameter {</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"> <span class="n" style="color: #333;">Parameter</span><span class="p">()</span> <span class="p">{</span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"> <span class="n" style="color: #333;">window_thresh</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//TODO check!</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"1.0.1<span class="idiff left right">0</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"1.0.1<span class="idiff left right">1</span>"</span><span class="p">;</span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"> <span class="n" style="color: #333;">huge_ins</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">999</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//TODO check??</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">Parameter</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">@@ -85,6 +85,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">skip_parameter_estimation</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">cs_string</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">read_strand</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">ccs_reads</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">set_regions</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">reg</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<li id="c758ea5b1649f4f7b6c0f8ba9660a877a95487e0">
<a href="https://salsa.debian.org/med-team/sniffles/commit/4cb082cc94b887ca4a4226c7af22a26b3e5f5302#c758ea5b1649f4f7b6c0f8ba9660a877a95487e0"><strong>src/Sniffles.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">@@ -95,6 +95,9 @@ void read_parameters(int argc, char *argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">TCLAP</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SwitchArg</span> <span class="n" style="color: #333;">arg_cs_string</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"cs_string"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Enables the scan of CS string instead of Cigar and MD. "</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</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="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">TCLAP</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SwitchArg</span> <span class="n" style="color: #333;">arg_read_strand</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"report_read_strands"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Enables the report of the strand categories per read. (Beta) "</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</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="LC97" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">TCLAP</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SwitchArg</span> <span class="n" style="color: #333;">arg_ccs</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"ccs_reads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Preset CCS Pacbio setting. (Beta) "</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"></span>
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98
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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">TCLAP</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ValueArg</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">arg_allelefreq</span><span class="p">(</span><span class="s" style="color: #d14;">"f"</span><span class="p">,</span> <span class="s" style="color: #d14;">"allelefreq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Threshold on allele frequency (0-1). "</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">"float"</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">);</span></span>
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99
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">TCLAP</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ValueArg</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">arg_hetfreq</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"min_het_af"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Threshold on allele frequency (0-1). "</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="s" style="color: #d14;">"float"</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">);</span></span>
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100
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">TCLAP</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ValueArg</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">arg_homofreq</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"min_homo_af"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Threshold on allele frequency (0-1). "</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="mf" style="color: #099;">0.8</span><span class="p">,</span> <span class="s" style="color: #d14;">"float"</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="143" 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="146" 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">@@ -143,6 +146,7 @@ void read_parameters(int argc, char *argv[]) {</td>
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143
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">printParameter</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="p">,</span> <span class="n" style="color: #333;">arg_seq</span><span class="p">);</span></span>
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144
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">printParameter</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="p">,</span> <span class="n" style="color: #333;">arg_std</span><span class="p">);</span></span>
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145
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">printParameter</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="p">,</span><span class="n" style="color: #333;">arg_read_strand</span><span class="p">);</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">printParameter</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="p">,</span><span class="n" style="color: #333;">arg_ccs</span><span class="p">);</span></span>
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146
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"></span>
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147
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">usage</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;">std</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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148
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">usage</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Parameter estimation:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="179" 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="183" 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">@@ -179,7 +183,7 @@ void read_parameters(int argc, char *argv[]) {</td>
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179
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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;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">change_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_coords</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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180
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">debug</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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181
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<td class="diff-line-num new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score_treshold</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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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">0bac61ef-7819-462b-ae3d-32c68fe580c0</span>"</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//21_16296949_+";//21_40181680_-";//m151102_123142_42286_c100922632550000001823194205121665_s1_p0/80643/0_20394"; //"22_36746138"; //just for debuging reasons!</span></span>
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<td class="diff-line-num new old_line" data-linenumber="183" 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="186" 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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left"> "</span></span><span class="p"><span class="idiff">;</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//m54238_180925_225123/56099701/ccs";//m54238_180926_231301/43516780/ccs</span>"; //21_16296949_+";//21_40181680_-";//m151102_123142_42286_c100922632550000001823194205121665_s1_p0/80643/0_20394"; //"22_36746138"; //just for debuging reasons!</span></span>
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<td class="diff-line-num old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
183
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<td class="diff-line-num new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bam_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;">arg_bamfile</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">());</span></span>
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184
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<td class="diff-line-num new_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_mq</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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185
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">output_vcf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_vcf</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="198" 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="202" 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">@@ -198,7 +202,7 @@ void read_parameters(int argc, char *argv[]) {</td>
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198
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<td class="diff-line-num new_line" data-linenumber="202" 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">
202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_segment_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_segsize</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="199" 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">
199
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<td class="diff-line-num new_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">reportBND</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_bnd</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="200" 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">
200
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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;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input_vcf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_input_vcf</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">print_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_seq</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="205" 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">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">print_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">true</span></span><span class="p"><span class="idiff">;</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//</span>arg_seq.getValue();</span></span>
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<td class="diff-line-num old_line" data-linenumber="202" 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">
202
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ignore_std</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_std</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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203
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_zmw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_zmw</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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204
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">homfreq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_homofreq</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="206" 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="210" 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">@@ -206,7 +210,13 @@ void read_parameters(int argc, char *argv[]) {</td>
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206
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">skip_parameter_estimation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_parameter</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
</pre>
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207
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cs_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_cs_string</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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208
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_strand</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">arg_read_strand</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="213" 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">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ccs_reads</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">arg_ccs</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ccs_reads</span><span class="p">){</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">skip_parameter_estimation</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="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ignore_std</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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209
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="p">}</span></span>
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210
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">skip_parameter_estimation</span><span class="p">)</span> <span class="p">{</span></span>
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211
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Skip parameter estimation."</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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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score_treshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="216" 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="226" 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">@@ -216,6 +226,7 @@ void read_parameters(int argc, char *argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">avg_ins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_insratio</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Parse IDS:</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*std::string buffer = arg_chrs.getValue();</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> int count = 0;</span></span>
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<a href="https://salsa.debian.org/med-team/sniffles/commit/4cb082cc94b887ca4a4226c7af22a26b3e5f5302#6559993eb064f711fc203323d78ac236f9ab998b"><strong>src/print/VCFPrinter.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">@@ -8,7 +8,7 @@</td>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "VCFPrinter.h"</span></span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"></span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">VCFPrinter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">print_header</span><span class="p">()</span> <span class="p">{</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##fileformat=VCFv4.<span class="idiff left right">3</span></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="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##fileformat=VCFv4.<span class="idiff left right">1</span></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="LC12" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##source=Sniffles</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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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">currentDateTime</span><span class="p">();</span></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##fileDate="</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 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">@@ -43,7 +43,7 @@ void VCFPrinter::print_header() {</td>
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=SVMETHOD,Number=1,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Type of approach used to detect SV</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=SVTYPE,Number=1,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Type of structural variant</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">report_n_reads</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;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">report_n_reads</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=RNAMES,Number=<span class="idiff left right">1</span>,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Names of reads supporting SVs (comma separated)</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=RNAMES,Number=<span class="idiff left right">.</span>,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Names of reads supporting SVs (comma separated)</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">print_seq</span><span class="p">)</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="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=SEQ,Number=1,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Extracted sequence from the best representative read.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" 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="54" 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">@@ -54,11 +54,11 @@ void VCFPrinter::print_header() {</td>
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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;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=REF_strand,Number=2,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">plus strand ref, minus strand ref.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <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>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=STD_quant_start,Number=A,Type=<span class="idiff left right">Integer</span>,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">STD of the start breakpoints across the reads.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=STD_quant_stop,Number=A,Type=<span class="idiff left right">Integer</span>,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">STD of the stop breakpoints across the reads.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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59
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<td class="diff-line-num new_line old" data-linenumber="57" 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="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=Kurtosis_quant_start,Number=A,Type=<span class="idiff left right">Integer</span>,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Kurtosis value of the start breakpoints across the reads.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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60
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<td class="diff-line-num new_line old" data-linenumber="57" 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="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=Kurtosis_quant_stop,Number=A,Type=<span class="idiff left right">Integer</span>,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Kurtosis value of the stop breakpoints across the reads.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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61
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<td class="diff-line-num new_line old" data-linenumber="57" 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="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=SUPTYPE,Number=<span class="idiff left right">1</span>,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Type by which the variant is supported.(SR,ALN,NR)</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="62" 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="57" 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">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=STD_quant_start,Number=A,Type=<span class="idiff left right">Float</span>,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">STD of the start breakpoints across the reads.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=STD_quant_stop,Number=A,Type=<span class="idiff left right">Float</span>,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">STD of the stop breakpoints across the reads.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=Kurtosis_quant_start,Number=A,Type=<span class="idiff left right">Float</span>,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Kurtosis value of the start breakpoints across the reads.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="60" 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">
60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=Kurtosis_quant_stop,Number=A,Type=<span class="idiff left right">Float</span>,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Kurtosis value of the stop breakpoints across the reads.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="61" 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">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=SUPTYPE,Number=<span class="idiff left right">A</span>,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Type by which the variant is supported.(SR,ALN,NR)</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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62
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<td class="diff-line-num new_line" data-linenumber="62" 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">
62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=STRANDS,Number=A,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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63
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<td class="diff-line-num new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=AF,Number=A,Type=Float,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Allele Frequency.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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64
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<td class="diff-line-num new_line" data-linenumber="64" 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">
64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=ZMW,Number=A,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Number of ZMWs (Pacbio) supporting SV.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" 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="106" 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">@@ -106,10 +106,11 @@ void VCFPrinter::print_body(Breakpoint * &SV, RefVector ref) {</td>
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<td class="diff-line-num old_line" data-linenumber="106" 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">
106
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="107" 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">
107
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IPrinter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">calc_pos</span><span class="p">(</span><span class="n" style="color: #333;">end_coord</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">chr</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="108" 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">
108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">strands</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_strand</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="LC109" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">fprintf</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"%s"</span></span><span class="p"><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">N</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="p"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"></span>
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">reportBND</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_SVtype</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">TRA</span><span class="p">))</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="c1" style="color: #998; font-style: italic;">//N[22:36765684[ +-</span></span>
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112
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//]21:10540232]N -+</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">N</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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113
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strands</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="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//&&</span></span>
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"]"</span><span class="p">);</span></span>
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">chr</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</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="125" 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">@@ -124,8 +125,22 @@ void VCFPrinter::print_body(Breakpoint * &SV, RefVector ref) {</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%c"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'['</span><span class="p">);</span></span>
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126
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC127" 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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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="p">}</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_sequence</span><span class="p">().</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_SVtype</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">INS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_SVtype</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">DEL</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%c"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">);</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_SVtype</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">DEL</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_sequence</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC132" 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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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%c"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">);</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="p">}</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%c"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">);</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_SVtype</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">INS</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_sequence</span><span class="p">().</span><span class="n" style="color: #333;">c_str</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 class="p">}</span> <span class="k" style="font-weight: 600;">else</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="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%c"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</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="p">}</span></span>
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128
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" 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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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">N</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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129
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%c"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'<'</span><span class="p">);</span></span>
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130
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">IPrinter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_type</span><span class="p">(</span><span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_SVtype</span><span class="p">()).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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131
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%c"</span><span class="p">,</span> <span class="sc" 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="145" 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="160" 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">@@ -145,16 +160,19 @@ void VCFPrinter::print_body(Breakpoint * &SV, RefVector ref) {</td>
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145
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"></span>
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146
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">";SVMETHOD=Snifflesv"</span><span class="p">);</span></span>
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147
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version</span><span class="p">.</span><span class="n" style="color: #333;">c_str</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>
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<td class="diff-line-num old_line" data-linenumber="148" 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">
148
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164
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<pre style="margin: 0;"> <span id="LC164" 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="p">(</span><span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">reportBND</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_SVtype</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">TRA</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">";CHR2="</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">chr</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">";END="</span><span class="p">);</span></span>
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (SV->get_SVtype() & INS) {</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fprintf(file, "%i", std::max((int) (end - SV->get_length()), start));</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//} else {</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">end</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="c1" style="color: #998; font-style: italic;">//}</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_SVtype</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">INS</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="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">));</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" 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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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="p">}</span></span>
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158
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"> <span class="p">}</span></span>
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159
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">zmws</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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160
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">";ZMW="</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="204" 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">@@ -186,11 +204,11 @@ void VCFPrinter::print_body(Breakpoint * &SV, RefVector ref) {</td>
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186
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"></span>
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187
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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;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_SVtype</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">INS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">huge_ins</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_types</span><span class="p">().</span><span class="n" style="color: #333;">is_ALN</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//!</span></span>
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188
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="mi" style="color: #099;">999999999</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="189" 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">
189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;"><span class="idiff left">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">SV</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">get_SVtype</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TRA</span></span><span class="p"><span class="idiff right">)</span>{</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span><span class="mi" style="color: #099;">0</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="p">}</span><span class="k" style="font-weight: 600;"><span class="idiff left">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">SV</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">get_SVtype</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">DEL</span></span><span class="p"><span class="idiff right">)</span>{</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;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_length</span><span class="p">()</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span>-</span><span class="mi" style="color: #099;">1</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 class="p">}</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="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="p">}</span><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="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SV</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">get_SVtype</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TRA</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span><span class="idiff left right"> </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="209" 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">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="p">}</span><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="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SV</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">get_SVtype</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">DEL</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_length</span><span class="p">()</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right"> </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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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="p">}</span><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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194
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_length</span><span class="p">());</span></span>
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195
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> <span class="p">}</span></span>
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196
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="226" 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="244" 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">@@ -226,10 +244,10 @@ void VCFPrinter::print_body(Breakpoint * &SV, RefVector ref) {</td>
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226
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_stop</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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227
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<td class="diff-line-num new_line" data-linenumber="245" 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">
245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="229" 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="LC229" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Parameter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Instance</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">print_seq</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_sequence</span><span class="p">().</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">";SEQ="</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="231" 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">
231
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_sequence</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="diff-line-num old old_line" data-linenumber="232" 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">
232
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp"> <span class="p">}</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// </span>if (Parameter::Instance()->print_seq && !SV->get_sequence().empty()) {</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// </span> fprintf(file, "%s", ";SEQ=");</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// </span> fprintf(file, "%s", SV->get_sequence().c_str());</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// </span>}</span></span>
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233
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="s" style="color: #d14;">";RE="</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="234" 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">
234
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">SV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_support</span><span class="p">());</span></span>
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235
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if(Parameter::Instance()->genotype){</span></span>
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