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

Nilesh Patra pushed to branch upstream at <a href="https://salsa.debian.org/med-team/tiddit">Debian Med / tiddit</a>

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

Commits:

</h4>

<ul>

<li>

<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/tiddit/-/commit/2a63d8ceac0ccb43d90344a9758a59fb83a7bc53">2a63d8ce</a></strong>

<div>

<span> by Nilesh Patra </span> <i> at 2023-05-11T22:51:38+05:30 </i>

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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 3.6.0+dfsg</pre>

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

4 changed files:

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<ul>

<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

</a>

</li>

<li class="file-stats">

<a href="#a4d6d5acd8b63bc82a7ede7695daeb65269ebbf9">

tiddit/__main__.py

</a>

</li>

<li class="file-stats">

<a href="#b8e0548d1ee3d872f60e8066825abdb509fd1456">

tiddit/tiddit_cluster.pyx

</a>

</li>

<li class="file-stats">

<a href="#21c5df89114f7a83af968a1fccf0399cbc349c35">

tiddit/tiddit_signal.pyx

</a>

</li>

</ul>

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

Changes:

</h4>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/tiddit/-/commit/2a63d8ceac0ccb43d90344a9758a59fb83a7bc53#8e2edce0d507e1297474f25c00cae94258db38d8"><strong style="font-weight: bold;">setup.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -20,7 +20,8 @@ else:</td>

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC21" class="line" lang="python"><span class="nf" style="color: #900; font-weight: 600;">setup</span><span class="p">(</span></span>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC22" class="line" lang="python">    <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'tiddit'</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="python">    <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.5.2'</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="python">    <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.6.0'</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

24

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC25" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC26" class="line" lang="python">    <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"https://github.com/SciLifeLab/TIDDIT"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC27" class="line" lang="python">    <span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Jesper Eisfeldt"</span><span class="p">,</span></span>

</pre></td>

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<br>

</li>

<li id="a4d6d5acd8b63bc82a7ede7695daeb65269ebbf9">

<a href="https://salsa.debian.org/med-team/tiddit/-/commit/2a63d8ceac0ccb43d90344a9758a59fb83a7bc53#a4d6d5acd8b63bc82a7ede7695daeb65269ebbf9"><strong style="font-weight: bold;">tiddit/__main__.py</strong></a>

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

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -17,7 +17,7 @@ import tiddit.tiddit_variant as tiddit_variant</td>

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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">tiddit.tiddit_contig_analysis</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tiddit_contig_analysis</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC18" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>

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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="python">       <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"3.<span class="idiff left right deletion" style="background-color: #fac5cd;">5.2</span>"</span></span>

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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="python">       <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"3.<span class="idiff left right addition" style="background-color: #c7f0d2;">6.0</span>"</span></span>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC21" class="line" lang="python">       <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">ArgumentParser</span><span class="p">(</span><span class="s" style="color: #d14;">"""tiddit-{}"""</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">),</span><span class="n" style="color: #333;">add_help</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC22" class="line" lang="python">       <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--sv"</span>    <span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"call structural variation"</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23" class="line" lang="python">       <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--cov"</span>        <span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"generate a coverage bed file"</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -155,7 +155,7 @@ def main():</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC155" class="line" lang="python">                      <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">library</span><span class="p">[</span><span class="s" style="color: #d14;">"avg_insert_size"</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="mf" style="color: #099;">2.0</span><span class="p">)</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC156" class="line" lang="python"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC157" class="line" lang="python">              <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">time</span><span class="p">()</span></span>

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<td class="old_line diff-line-num old" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC158" class="line" lang="python">              <span class="n" style="color: #333;">sv_clusters</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tiddit_cluster</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span><span class="n" style="color: #333;">contigs</span><span class="p">,</span><span class="n" style="color: #333;">contig_length</span><span class="p">,</span><span class="n" style="color: #333;">samples</span><span class="p">,</span><span class="n" style="color: #333;">library</span><span class="p">[</span><span class="s" style="color: #d14;">"mp"</span><span class="p">],</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">e</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">l</span><span class="p">,</span><span class="n" style="color: #333;">max_ins_len</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_contig</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">skip_assembly</span><span class="p">)</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC158" class="line" lang="python">              <span class="n" style="color: #333;">sv_clusters</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tiddit_cluster</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span><span class="n" style="color: #333;">contigs</span><span class="p">,</span><span class="n" style="color: #333;">contig_length</span><span class="p">,</span><span class="n" style="color: #333;">samples</span><span class="p">,</span><span class="n" style="color: #333;">library</span><span class="p">[</span><span class="s" style="color: #d14;">"mp"</span><span class="p">],</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">e</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">l</span><span class="p">,</span><span class="n" style="color: #333;">max_ins_len</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_contig</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">skip_assembly</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">args</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">r</span></span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC159" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC160" class="line" lang="python">              <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"generated clusters in"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="161" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="161" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC161" class="line" lang="python">              <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">time</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">t</span><span class="p">)</span></span>

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<br>

</li>

<li id="b8e0548d1ee3d872f60e8066825abdb509fd1456">

<a href="https://salsa.debian.org/med-team/tiddit/-/commit/2a63d8ceac0ccb43d90344a9758a59fb83a7bc53#b8e0548d1ee3d872f60e8066825abdb509fd1456"><strong style="font-weight: bold;">tiddit/tiddit_cluster.pyx</strong></a>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -37,7 +37,7 @@ def find_discordant_pos(fragment,is_mp):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC37" class="line" lang="cython"></span>

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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC38" class="line" lang="cython">       <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">posA</span><span class="p">,</span><span class="n" style="color: #333;">posB</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="cython"></span>

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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC40" class="line" lang="cython"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span><span class="n" style="color: #333;">chromosomes</span><span class="p">,</span><span class="n" style="color: #333;">contig_length</span><span class="p">,</span><span class="n" style="color: #333;">samples</span><span class="p">,</span><span class="n" style="color: #333;">is_mp</span><span class="p">,</span><span class="n" style="color: #333;">epsilon</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">,</span><span class="n" style="color: #333;">max_ins_len</span><span class="p">,</span><span class="n" style="color: #333;">min_contig</span><span class="p">,</span><span class="n" style="color: #333;">skip_assembly</span><span class="p">):</span></span>

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<td class="old_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="cython"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span><span class="n" style="color: #333;">chromosomes</span><span class="p">,</span><span class="n" style="color: #333;">contig_length</span><span class="p">,</span><span class="n" style="color: #333;">samples</span><span class="p">,</span><span class="n" style="color: #333;">is_mp</span><span class="p">,</span><span class="n" style="color: #333;">epsilon</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">,</span><span class="n" style="color: #333;">max_ins_len</span><span class="p">,</span><span class="n" style="color: #333;">min_contig</span><span class="p">,</span><span class="n" style="color: #333;">skip_assembly</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">min_reads</span></span><span class="p">):</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC41" class="line" lang="cython"></span>

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<td class="old_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC42" class="line" lang="cython">       <span class="n" style="color: #333;">discordants</span><span class="o" style="font-weight: 600;">=</span><span class="p">{}</span></span>

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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC43" class="line" lang="cython">       <span class="n" style="color: #333;">contigs</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">set</span><span class="p">([])</span></span>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -265,13 +265,18 @@ def main(prefix,chromosomes,contig_length,samples,is_mp,epsilon,m,max_ins_len,mi</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC265" class="line" lang="cython">                              <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"N_splits"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"splits"</span><span class="p">])</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC266" class="line" lang="cython">                              <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"N_contigs"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"contigs"</span><span class="p">])</span></span>

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<td class="new_line diff-line-num old" data-linenumber="268" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC268" class="line" lang="cython">                              <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"N_contigs"</span><span class="p">]:</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC268" class="line" lang="cython"></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC269" class="line" lang="cython">                              <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"N_splits"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">min_reads</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"N_splits"</span><span class="p">]:</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC270" class="line" lang="cython">                                      <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"posA"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">mode</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"positions_A"</span><span class="p">][</span><span class="s" style="color: #d14;">"splits"</span><span class="p">])</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC271" class="line" lang="cython">                                      <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"posB"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">mode</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"positions_B"</span><span class="p">][</span><span class="s" style="color: #d14;">"splits"</span><span class="p">])</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC273" class="line" lang="cython">                              <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"N_contigs"</span><span class="p">]:</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC274" class="line" lang="cython">                                      <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"posA"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">mode</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"positions_A"</span><span class="p">][</span><span class="s" style="color: #d14;">"contigs"</span><span class="p">])</span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC275" class="line" lang="cython">                                      <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"posB"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">mode</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"positions_B"</span><span class="p">][</span><span class="s" style="color: #d14;">"contigs"</span><span class="p">])</span></span>

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<td class="old_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC276" class="line" lang="cython"></span>

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<td class="old_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC277" class="line" lang="cython">                              <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"N_splits"</span><span class="p">]:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

272

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<td class="new_line diff-line-num" data-linenumber="278" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC278" class="line" lang="cython">                                      <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"posA"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">mode</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"positions_A"</span><span class="p">][</span><span class="s" style="color: #d14;">"splits"</span><span class="p">])</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC273" class="line" lang="cython">                                      <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"posB"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">mode</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"positions_B"</span><span class="p">][</span><span class="s" style="color: #d14;">"splits"</span><span class="p">])</span></span>

</pre></td>

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<td class="new_line diff-line-num old" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC274" class="line" lang="cython"></span>

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<td class="old_line diff-line-num new" data-linenumber="275" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC279" class="line" lang="cython">                                      <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"posB"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">mode</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"positions_B"</span><span class="p">][</span><span class="s" style="color: #d14;">"splits"</span><span class="p">])</span>                             </span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC280" class="line" lang="cython"></span>

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<td class="new_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC281" class="line" lang="cython">                              <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="new_line diff-line-num" data-linenumber="282" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC282" class="line" lang="cython">                                      <span class="n" style="color: #333;">reverse_A</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"positions_A"</span><span class="p">][</span><span class="s" style="color: #d14;">"orientation_discordants"</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"True"</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="328" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="333" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -328,10 +333,6 @@ def main(prefix,chromosomes,contig_length,samples,is_mp,epsilon,m,max_ins_len,mi</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC333" class="line" lang="cython">                                              <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"posB"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">mode</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"positions_B"</span><span class="p">][</span><span class="s" style="color: #d14;">"discordants"</span><span class="p">])</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC335" class="line" lang="cython"></span>

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<td class="new_line diff-line-num old" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC331" class="line" lang="cython"></span>

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<td class="new_line diff-line-num old" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC332" class="line" lang="cython">                                      <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"posA"</span><span class="p">]</span></span>

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<td class="old_line diff-line-num old" data-linenumber="333" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC333" class="line" lang="cython">                                      <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"posB"</span><span class="p">]</span></span>

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<td class="old_line diff-line-num old" data-linenumber="334" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC334" class="line" lang="cython"></span>

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<td class="new_line diff-line-num" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC336" class="line" lang="cython">                              <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"startB"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"positions_B"</span><span class="p">][</span><span class="s" style="color: #d14;">"start"</span><span class="p">])</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC337" class="line" lang="cython">                              <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"endB"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">][</span><span class="n" style="color: #333;">chrB</span><span class="p">][</span><span class="n" style="color: #333;">candidate</span><span class="p">][</span><span class="s" style="color: #d14;">"positions_B"</span><span class="p">][</span><span class="s" style="color: #d14;">"end"</span><span class="p">])</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC338" class="line" lang="cython"></span>

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<li id="21c5df89114f7a83af968a1fccf0399cbc349c35">

<a href="https://salsa.debian.org/med-team/tiddit/-/commit/2a63d8ceac0ccb43d90344a9758a59fb83a7bc53#21c5df89114f7a83af968a1fccf0399cbc349c35"><strong style="font-weight: bold;">tiddit/tiddit_signal.pyx</strong></a>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -65,7 +65,13 @@ def SA_analysis(read,min_q,tag,reference_name):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC65" class="line" lang="cython"></span>

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<td class="new_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC66" class="line" lang="cython">       <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">read_query_alignment_end</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_end</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC67" class="line" lang="cython"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

68

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC68" class="line" lang="cython">       <span class="nf" style="color: #900; font-weight: 600;">if </span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_start</span> <span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">read_query_alignment_end</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

68

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC68" class="line" lang="cython">       <span class="n" style="color: #333;">clip_before</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span></span>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

69

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC69" class="line" lang="cython"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

70

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC70" class="line" lang="cython">       <span class="n" style="color: #333;">supplementry_alignment</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">find_SA_query_range</span><span class="p">(</span><span class="n" style="color: #333;">SA_data</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

71

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="cython">       <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">supplementry_alignment</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_start</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_start</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

72

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC72" class="line" lang="cython">               <span class="n" style="color: #333;">clip_before</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span></span>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

73

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC73" class="line" lang="cython"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

74

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC74" class="line" lang="cython">       <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">clip_before</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

69

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<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

75

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC75" class="line" lang="cython">               <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">is_reverse</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

70

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<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

76

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC76" class="line" lang="cython"></span>

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<td class="old_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

71

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<td class="new_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

77

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC77" class="line" lang="cython"></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -78,7 +84,6 @@ def SA_analysis(read,min_q,tag,reference_name):</td>

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<td class="new_line diff-line-num" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

84

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC84" class="line" lang="cython">               <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

79

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<td class="new_line diff-line-num" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

85

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC85" class="line" lang="cython">                       <span class="n" style="color: #333;">split_pos</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">reference_start</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span></span>

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<td class="old_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

80

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<td class="new_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC81" class="line" lang="cython">       <span class="n" style="color: #333;">supplementry_alignment</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">find_SA_query_range</span><span class="p">(</span><span class="n" style="color: #333;">SA_data</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC87" class="line" lang="cython">       <span class="n" style="color: #333;">SA_chr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">SA_data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC88" class="line" lang="cython"></span>

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<td class="new_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC89" class="line" lang="cython">       <span class="n" style="color: #333;">startA</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">reference_start</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -87,8 +92,7 @@ def SA_analysis(read,min_q,tag,reference_name):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC92" class="line" lang="cython">       <span class="n" style="color: #333;">startB</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">supplementry_alignment</span><span class="p">.</span><span class="n" style="color: #333;">reference_start</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC93" class="line" lang="cython">       <span class="n" style="color: #333;">endB</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">supplementry_alignment</span><span class="p">.</span><span class="n" style="color: #333;">reference_end</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC94" class="line" lang="cython"></span>

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<td class="new_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC90" class="line" lang="cython"></span>

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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC91" class="line" lang="cython">       <span class="nf" style="color: #900; font-weight: 600;">if </span><span class="p">(</span><span class="n" style="color: #333;">supplementry_alignment</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_start</span> <span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">supplementry_alignment</span><span class="p">.</span><span class="n" style="color: #333;">query_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">read_query_alignment_end</span><span class="p">):</span></span>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC95" class="line" lang="cython">       <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clip_before</span><span class="p">:</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC96" class="line" lang="cython">               <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">SA_data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC97" class="line" lang="cython"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC98" class="line" lang="cython">                       <span class="n" style="color: #333;">SA_split_pos</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">supplementry_alignment</span><span class="p">.</span><span class="n" style="color: #333;">reference_start</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="192" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -192,6 +196,9 @@ def worker(str chromosome, str bam_file_name,str ref,str prefix,int min_q,int ma</td>

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<td class="old_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

192

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<td class="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

196

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC196" class="line" lang="cython">              <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">mate_is_unmapped</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

193

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<td class="new_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

197

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC197" class="line" lang="cython">                      <span class="k" style="font-weight: 600;">continue</span></span>

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<td class="old_line diff-line-num" data-linenumber="194" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

194

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<td class="new_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

198

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC198" class="line" lang="cython"></span>

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<td class="old_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

199

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC199" class="line" lang="cython">              <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">is_paired</span><span class="p">:</span></span>

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<td class="old_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

200

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC200" class="line" lang="cython">                      <span class="k" style="font-weight: 600;">continue</span></span>

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<td class="old_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

201

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC201" class="line" lang="cython"></span>

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<td class="old_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

202

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC202" class="line" lang="cython"></span>

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<td class="old_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC203" class="line" lang="cython">              <span class="nf" style="color: #900; font-weight: 600;">if </span><span class="p">(</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">isize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_ins</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">mate_chromosome</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">read_chromosome</span> <span class="p">):</span></span>

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<td class="old_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

197

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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC204" class="line" lang="cython">                      <span class="n" style="color: #333;">read_query_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_name</span></span>

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