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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Andreas Tille pushed to branch upstream at <a href="https://salsa.debian.org/med-team/mosdepth">Debian Med / mosdepth</a>
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Commits:
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/mosdepth/-/commit/0ba1c572ff9b8df67fd5a3786aeea97b00dca570">0ba1c572</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2024-12-13T16:05:21+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu 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 0.3.10+ds</pre>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
8 changed files:
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<li class="file-stats">
<a href="#4123588cdef112aa874bf52a300e9ed01db3ccd2">
<span class="new-file">
+
.github/FUNDING.yml
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<li class="file-stats">
<a href="#fe77d5d1439f26e353a42bbd38dece2467ff6558">
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+
.github/workflows/build.yml
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<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#98f5d7ecd16412a1f8781d3d8c896dd0323a69af">
depthstat.nim
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<li class="file-stats">
<a href="#5e05ccb32e2de6797c54768d95e4cc3ba8c8bc5f">
functional-tests.sh
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<li class="file-stats">
<a href="#f2a4f454974b64d881d2a470683d1c37fb1aa2bb">
mosdepth.nim
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<li class="file-stats">
<a href="#a99b7e9ffb6c06b4832f1c7ce8d8dbbf023f7502">
mosdepth.nimble
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Changes:
</h4>
<li id="4123588cdef112aa874bf52a300e9ed01db3ccd2">
<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/0ba1c572ff9b8df67fd5a3786aeea97b00dca570#4123588cdef112aa874bf52a300e9ed01db3ccd2"><strong style="font-weight: 600;">.github/FUNDING.yml</strong></a>
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC1" class="line" lang="yaml"><span class="c1" style="color: #999988; font-style: italic;"># These are supported funding model platforms</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC2" class="line" lang="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">github</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">brentp</span><span class="pi">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">patreon</span><span class="pi">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Replace with a single Patreon username</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.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="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">open_collective</span><span class="pi">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Replace with a single Open Collective username</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.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="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">ko_fi</span><span class="pi">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Replace with a single Ko-fi username</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.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="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">tidelift</span><span class="pi">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Replace with a single Tidelift platform-name/package-name e.g., npm/babel</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.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="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">community_bridge</span><span class="pi">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Replace with a single Community Bridge project-name e.g., cloud-foundry</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.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="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">liberapay</span><span class="pi">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Replace with a single Liberapay username</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.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="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC10" class="line" lang="yaml"><span class="na" style="color: #008080;">issuehunt</span><span class="pi">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Replace with a single IssueHunt username</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.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="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
11
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">otechie</span><span class="pi">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Replace with a single Otechie username</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.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="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
12
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">lfx_crowdfunding</span><span class="pi">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Replace with a single LFX Crowdfunding project-name e.g., cloud-foundry</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.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="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">custom</span><span class="pi">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Replace with up to 4 custom sponsorship URLs e.g., ['link1', 'link2']</span></span></pre></td>
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<li id="fe77d5d1439f26e353a42bbd38dece2467ff6558">
<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/0ba1c572ff9b8df67fd5a3786aeea97b00dca570#fe77d5d1439f26e353a42bbd38dece2467ff6558"><strong style="font-weight: 600;">.github/workflows/build.yml</strong></a>
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1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC1" class="line" lang="yaml"><span class="c1" style="color: #999988; font-style: italic;"># copied from Daniel Cook's Seq collection</span></span>
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2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Build</span></span>
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3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC3" class="line" lang="yaml"></span>
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4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span> </span>
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5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">push</span><span class="pi">:</span></span>
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6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #dd1144;">master</span></span>
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8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">pull_request</span><span class="pi">:</span></span>
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9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #dd1144;">master</span></span>
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11
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC11" class="line" lang="yaml"></span>
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12
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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14
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC14" class="line" lang="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">${{ matrix.os }}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">fail-fast</span><span class="pi">:</span> <span class="kc" style="font-weight: 600;">false</span></span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">ubuntu-20.04</span><span class="pi">,</span> <span class="nv" style="color: #008080;">macos-13</span><span class="pi">]</span></span>
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20
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span></span>
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21
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22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="pi">-</span> <span class="s" style="color: #dd1144;">2.0.2</span></span>
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23
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24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">actions/checkout@v4</span></span>
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27
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC28" class="line" lang="yaml"> <span class="c1" style="color: #999988; font-style: italic;"># Caching</span></span>
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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Cache choosenim</span></span>
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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
30
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">id</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">cache-choosenim</span></span>
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31
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">actions/cache@v4</span></span>
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32
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
33
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">~/.choosenim</span></span>
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">key</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">${{ runner.os }}-choosenim-stable</span></span>
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35
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC35" class="line" lang="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
36
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Cache nimble</span></span>
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">id</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">cache-nimble</span></span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">actions/cache@v4</span></span>
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39
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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40
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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">key</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">${{ runner.os }}-nimble-stable</span></span>
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42
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Cache htslib</span></span>
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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
44
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">id</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">cache-htslib</span></span>
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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
45
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC45" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">actions/cache@v4</span></span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
46
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC46" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
47
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">$HOME/htslib</span></span>
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">key</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">${{ runner.os }}-htslib-1.10</span></span>
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49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC49" class="line" lang="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC50" class="line" lang="yaml"> <span class="c1" style="color: #999988; font-style: italic;"># Install Dependencies</span></span>
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51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC51" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Install dependencies (Linux)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
52
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">runner.os == 'Linux'</span></span>
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53
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC54" class="line" lang="yaml"> <span class="s" style="color: #dd1144;">sudo apt-get update</span></span>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC55" class="line" lang="yaml"> <span class="s" style="color: #dd1144;">sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \</span></span>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC56" class="line" lang="yaml"> <span class="s" style="color: #dd1144;">curl libssl-dev libtool autoconf automake libcurl4-openssl-dev zlib1g-dev</span></span>
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57
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC57" class="line" lang="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC58" class="line" lang="yaml"> <span class="c1" style="color: #999988; font-style: italic;"># Setup htslib</span></span>
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59
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC59" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Install htslib (linux)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC60" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">runner.os == 'Linux'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC61" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC62" class="line" lang="yaml"> <span class="s" style="color: #dd1144;">cd</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC63" class="line" lang="yaml"> <span class="s" style="color: #dd1144;">git clone -b 1.18 --recursive https://github.com/samtools/htslib.git</span></span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC64" class="line" lang="yaml"> <span class="s" style="color: #dd1144;">cd htslib && autoheader && autoconf && ./configure --enable-libcurl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="s" style="color: #dd1144;">sudo make -j 4 install</span></span>
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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
66
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="s" style="color: #dd1144;">sudo ldconfig</span></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="s" style="color: #dd1144;">#echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="s" style="color: #dd1144;">#ls -lh $HOME/htslib/*.so</span></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Install hstlib (macos)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">runner.os == 'macOS'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="s" style="color: #dd1144;">brew install htslib</span></span>
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Set DYLD_LIBRARY_PATH</span></span>
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
76
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">runner.os == 'macOS'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
77
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC78" class="line" lang="yaml"> <span class="s" style="color: #dd1144;">echo "DYLD_LIBRARY_PATH=$(brew --prefix htslib)/lib" >> $GITHUB_ENV</span></span>
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC79" class="line" lang="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
80
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC80" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Install d4</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
81
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
82
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC82" class="line" lang="yaml"> <span class="s" style="color: #dd1144;">#export HTSLIB=system</span></span>
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
83
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC83" class="line" lang="yaml"> <span class="s" style="color: #dd1144;">git clone https://github.com/38/d4-format</span></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="s" style="color: #dd1144;">echo 'location' >> ~/.curlrc # https://github.com/38/d4-format/pull/77#issuecomment-2044438359</span></span>
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="s" style="color: #dd1144;">cd d4-format</span></span>
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC86" class="line" lang="yaml"> <span class="s" style="color: #dd1144;">cargo build --release --all-features --package=d4binding</span></span>
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="s" style="color: #dd1144;">sudo cp target/release/libd4binding.* /usr/local/lib</span></span>
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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
88
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="s" style="color: #dd1144;">sudo cp d4binding/include/d4.h /usr/local/include/</span></span>
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="s" style="color: #dd1144;">sudo ldconfig || true</span></span>
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90
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
91
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
92
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">iffy/install-nim@v5</span></span>
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
94
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">${{ matrix.version }}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
95
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
96
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Rust Toolchain</span></span>
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97
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">dtolnay/rust-toolchain@nightly</span></span>
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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC99" class="line" lang="yaml"> <span class="na" style="color: #008080;">toolchain</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">stable</span></span>
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100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC100" class="line" lang="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC101" class="line" lang="yaml"> <span class="c1" style="color: #999988; font-style: italic;"># Build and Test</span></span>
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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC102" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Build test executable</span></span>
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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
103
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC103" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">nimble build -Y mosdepth.nimble</span></span>
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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
104
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC104" class="line" lang="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
105
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC105" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Copy</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #dd1144;">binary"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
106
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC106" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">chmod +x mosdepth && mkdir bin && cp mosdepth bin/mosdepth_debug_${{ matrix.os }}</span></span>
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107
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC107" class="line" lang="yaml"></span>
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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC108" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Build</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #dd1144;">and</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #dd1144;">Copy</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #dd1144;">release</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #dd1144;">binary"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
109
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC109" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">nim c --mm:refc -d:danger -d:release -o:bin/mosdepth_${{ matrix.os }} mosdepth</span></span>
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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC110" class="line" lang="yaml"> </span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC111" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Functional Tests</span></span>
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<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC112" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC113" class="line" lang="yaml"> <span class="na" style="color: #008080;">TERM</span><span class="pi">:</span> <span class="s2" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">xterm"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
114
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC114" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
115
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC115" class="line" lang="yaml"> <span class="s" style="color: #dd1144;">bash ./functional-tests.sh</span></span>
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117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC117" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Unit Tests</span></span>
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118
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC118" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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119
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC119" class="line" lang="yaml"> <span class="s" style="color: #dd1144;">nim c -r tests/all.nim</span></span>
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120
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121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC121" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">Upload Artifact</span></span>
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122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC122" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">success()</span></span>
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123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC123" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">actions/upload-artifact@v4</span></span>
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124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC124" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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125
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC125" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">mosdepth_${{ matrix.os }}_nim${{ matrix.version }}_executable</span></span>
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126
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC126" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #dd1144;">bin/</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/0ba1c572ff9b8df67fd5a3786aeea97b00dca570#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong style="font-weight: 600;">CHANGES.md</strong></a>
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1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">v0.3.10</span></span>
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2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=======</span></span>
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3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC3" class="line" lang="markdown"><span class="p">+</span> write sfi index in d4 files (#243)</span>
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4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC4" class="line" lang="markdown"></span>
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5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">v0.3.9</span></span>
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6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">======</span></span>
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7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC7" class="line" lang="markdown"><span class="p">+</span> fix d4 output (#237)</span>
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8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">v0.3.8</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">======</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC11" class="line" lang="markdown"><span class="p">+</span> mosdepth is now much faster on bams/crams with a large number of contigs (#229)</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">v0.3.7</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">======</span></span>
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15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC15" class="line" lang="markdown"><span class="p">+</span> support CRAM v3.1. only updates htslib that binary is built with to v1.19.1 (#224)</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">v0.3.6</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"><span class="p">+</span> allow filtering on fragment length thanks @LudvigOlsen for implementing! (#214)</span>
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<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/0ba1c572ff9b8df67fd5a3786aeea97b00dca570#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong style="font-weight: 600;">README.md</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -4,9 +4,7 @@ fast BAM/CRAM depth calculation for **WGS**, **exome**, or **targeted sequencing</td>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build</span><span class="p">](</span><span class="sx" style="color: #dd1144;">https://github.com/brentp/mosdepth/workflows/Build/badge.svg?branch=master</span><span class="p">)</span>](https://github.com/brentp/mosdepth/actions?query=workflow%3ABuild)</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![citation</span><span class="p">](</span><span class="sx" style="color: #dd1144;">https://img.shields.io/badge/cite-open%20access-orange.svg</span><span class="p">)</span>](https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btx699/4583630?guestAccessKey=35b55064-4566-4ab3-a769-32916fa1c6e6)</span>
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7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build</span><span class="p">](</span><span class="sx" style="color: #dd1144;">https://github.com/brentp/mosdepth/actions/workflows/build.yml/badge.svg</span><span class="p">)</span>](https://github.com/brentp/mosdepth/actions/workflows/build.yml) <span class="p">[</span><span class="nv" style="color: #008080;">![citation</span><span class="p">](</span><span class="sx" style="color: #dd1144;">https://img.shields.io/badge/cite-open%20access-orange.svg</span><span class="p">)</span>](https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btx699/4583630?guestAccessKey=35b55064-4566-4ab3-a769-32916fa1c6e6)</span>
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10
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC8" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
11
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC9" class="line" lang="markdown"><span class="sb" style="color: #dd1144;">`mosdepth`</span> can output:</span>
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12
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10
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC10" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.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="23" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -25,7 +23,7 @@ when appropriate, the output files are bgzipped and indexed for ease of use.</td>
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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
25
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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## usage</span></span>
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26
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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
24
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"></span>
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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
27
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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
25
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"><span class="p">```</span></span>
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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
28
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<td class="new_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC28" class="line" lang="markdown">mosdepth 0.3.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span></span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown">mosdepth 0.3.<span class="idiff left right addition" style="background-color: #c7f0d2;">9</span></span>
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29
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<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
27
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"></span>
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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
30
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<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
28
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC28" class="line" lang="markdown"> Usage: mosdepth [options] <prefix> <BAM-or-CRAM></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC29" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.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="31" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -33,8 +31,7 @@ Arguments:</td>
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33
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31
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC31" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
34
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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
32
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC32" class="line" lang="markdown"> <prefix> outputs: `{prefix}.mosdepth.global.dist.txt`</span>
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35
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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
33
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC33" class="line" lang="markdown"> `{prefix}.mosdepth.summary.txt`</span>
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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
36
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<td class="new_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC36" class="line" lang="markdown"> `{prefix}.mosdepth.region.dist.txt` (if --by is specified)</span>
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<td class="old_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
37
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<td class="new_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"> `{prefix}.per-base.bed.gz|per-base.d4` (unless -n/--no-per-base is specified)</span>
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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.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="34" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC34" class="line" lang="markdown"> `{prefix}.per-base.bed.gz` (unless -n/--no-per-base is specified)</span>
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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
38
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<td class="new_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
35
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC35" class="line" lang="markdown"> `{prefix}.regions.bed.gz` (if --by is specified)</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC36" class="line" lang="markdown"> `{prefix}.quantized.bed.gz` (if --quantize is specified)</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"> `{prefix}.thresholds.bed.gz` (if --thresholds is specified)</span>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -43,29 +40,29 @@ Arguments:</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"></span>
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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
41
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown">Common Options:</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
46
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<td class="new_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC46" class="line" lang="markdown"> -t --threads <threads> number of BAM decompression threads<span class="idiff left right deletion" style="background-color: #fac5cd;">. (use 4 or fewer)</span> [default: 0]</span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"> -t --threads <threads> number of BAM decompression threads [default: 0]</span>
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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
47
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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
44
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC44" class="line" lang="markdown"> -c --chrom <chrom> chromosome to restrict depth calculation.</span>
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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
48
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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
45
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC45" class="line" lang="markdown"> -b --by <bed|window> optional BED file or (integer) window-sizes.</span>
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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
46
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC46" class="line" lang="markdown"> -n --no-per-base dont output per-base depth. skipping this output will speed execution</span>
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50
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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
47
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC47" class="line" lang="markdown"> substantially. prefer quantized or thresholded values if possible.</span>
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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
51
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<td class="new_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC51" class="line" lang="markdown"> -f --fasta <fasta> fasta file for use with CRAM files.</span>
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<td class="new_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC52" class="line" lang="markdown"> --d4 output per-base depth in d4 format. This is much faster.</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC53" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC48" class="line" lang="markdown"> -f --fasta <fasta> fasta file for use with CRAM files [default: ].</span>
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC49" class="line" lang="markdown"> --d4 output per-base depth in d4 format.</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC50" class="line" lang="markdown"></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC51" class="line" lang="markdown">Other options:</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC52" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(5,5,6,.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="53" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC57" class="line" lang="markdown"> -F --flag <FLAG> exclude reads with any of the bits in FLAG set [default: 1796]</span>
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58
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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC58" class="line" lang="markdown"> -i --include-flag <FLAG> only include reads with any of the bits in FLAG set. default is unset. [default: 0]</span>
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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
59
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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC59" class="line" lang="markdown"> -x --fast-mode dont look at internal cigar operations or correct mate overlaps (recommended for most use-cases).</span>
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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
60
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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC60" class="line" lang="markdown"> -q --quantize <segments> write quantized output see docs for description.</span>
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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
61
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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC61" class="line" lang="markdown"> -Q --mapq <mapq> mapping quality threshold. reads with a mapping quality less than this are ignored [default: 0]</span>
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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
62
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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC62" class="line" lang="markdown"> -T --thresholds <thresholds> for each interval in --by, write number of bases covered by at</span>
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<td class="old_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
63
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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC63" class="line" lang="markdown"> least threshold bases. Specify multiple integer values separated</span>
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<td class="old_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
64
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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC64" class="line" lang="markdown"> by ','.</span>
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<td class="old_line diff-line-num old" data-linenumber="65" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
65
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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"> -m --use-median output median of each region (in --by) instead of mean.</span>
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<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
66
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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"> -R --read-groups <string> only calculate depth for these comma-separated read groups IDs.</span>
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<td class="old_line diff-line-num old" data-linenumber="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
67
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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"> -h --help show help</span>
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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(5,5,6,.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="53" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"></span>
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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.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="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
53
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC53" class="line" lang="markdown"> -F --flag <FLAG> exclude reads with any of the bits in FLAG set [default: 1796]</span>
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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.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="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC54" class="line" lang="markdown"> -i --include-flag <FLAG> only include reads with any of the bits in FLAG set. default is unset. [default: 0]</span>
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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.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="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC55" class="line" lang="markdown"> -x --fast-mode dont look at internal cigar operations or correct mate overlaps (recommended for most use-cases).</span>
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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.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="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC56" class="line" lang="markdown"> -q --quantize <segments> write quantized output see docs for description.</span>
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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.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="57" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
57
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC57" class="line" lang="markdown"> -Q --mapq <mapq> mapping quality threshold. reads with a quality less than this value are ignored [default: 0]</span>
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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.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="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC58" class="line" lang="markdown"> -l --min-frag-len <min-frag-len> minimum insert size. reads with a smaller insert size than this are ignored [default: -1]</span>
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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.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="59" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
59
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC59" class="line" lang="markdown"> -u --max-frag-len <max-frag-len> maximum insert size. reads with a larger insert size than this are ignored. [default: -1]</span>
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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.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="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC60" class="line" lang="markdown"> -T --thresholds <thresholds> for each interval in --by, write number of bases covered by at</span>
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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.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="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC61" class="line" lang="markdown"> least threshold bases. Specify multiple integer values separated</span>
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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC62" class="line" lang="markdown"> by ','.</span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC63" class="line" lang="markdown"> -m --use-median output median of each region (in --by) instead of mean.</span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC64" class="line" lang="markdown"> -R --read-groups <string> only calculate depth for these comma-separated read groups IDs.</span>
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"> -h --help show help</span>
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69
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<td class="new_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
66
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown"><span class="p">```</span></span>
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<td class="old_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(5,5,6,.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="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
67
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="markdown">If you use mosdepth please cite <span class="p">[</span><span class="nv" style="color: #008080;">the publication in bioinformatics</span><span class="p">](</span><span class="sx" style="color: #dd1144;">https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btx699/4583630?guestAccessKey=35b55064-4566-4ab3-a769-32916fa1c6e6</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/0ba1c572ff9b8df67fd5a3786aeea97b00dca570#98f5d7ecd16412a1f8781d3d8c896dd0323a69af"><strong style="font-weight: 600;">depthstat.nim</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -15,12 +15,10 @@ proc initCountStat*[T](size:int=32768): CountStat[T] =</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC15" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
16
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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
16
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC16" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #990000; font-weight: 600;">add</span><span class="o" style="font-weight: 600;">*[</span><span class="n" style="color: #333333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333333;">c</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">CountStat</span><span class="p">,</span> <span class="n" style="color: #333333;">value</span><span class="p">:</span> <span class="n" style="color: #333333;">T</span><span class="p">)</span> <span class="p">{.</span><span class="n" style="color: #333333;">inline</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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17
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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
17
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"> <span class="n" style="color: #333333;">c</span><span class="p">.</span><span class="n" style="color: #333333;">n</span><span class="p">.</span><span class="n" style="color: #333333;">inc</span></span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">value</span><span class="p">.</span><span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333333;">c</span><span class="p">.</span><span class="n" style="color: #333333;">counts</span><span class="p">.</span><span class="n" style="color: #333333;">high</span><span class="p">.</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"> <span class="n" style="color: #333333;">c</span><span class="p">.</span><span class="n" style="color: #333333;">counts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">c</span><span class="p">.</span><span class="n" style="color: #333333;">counts</span><span class="p">.</span><span class="n" style="color: #333333;">high</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333333;">inc</span></span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
20
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<td class="new_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333333;">value</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #009999;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.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="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">value</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #009999;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
21
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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
19
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333333;">newException</span><span class="p">(</span><span class="n" style="color: #333333;">IndexDefect</span><span class="p">,</span> <span class="s" style="color: #dd1144;">"error setting negative depth value:"</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333333;">value</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(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
22
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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
20
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"> <span class="n" style="color: #333333;">c</span><span class="p">.</span><span class="n" style="color: #333333;">counts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">value</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333333;">inc</span></span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"> <span class="n" style="color: #333333;">c</span><span class="p">.</span><span class="n" style="color: #333333;">counts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">min</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">c</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">counts</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">high</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">T</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;">value</span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333333;">inc</span></span>
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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #990000; font-weight: 600;">median</span><span class="o" style="font-weight: 600;">*[</span><span class="n" style="color: #333333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333333;">c</span><span class="p">:</span> <span class="n" style="color: #333333;">CountStat</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">):</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="p">{.</span><span class="n" style="color: #333333;">inline</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(5,5,6,.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="24" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">stop_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="p">(</span><span class="mf" style="color: #009999;">0.5</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">c</span><span class="p">.</span><span class="n" style="color: #333333;">n</span><span class="p">.</span><span class="kt" style="color: #445588; font-weight: 600;">float64</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #009999;">0.5</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/0ba1c572ff9b8df67fd5a3786aeea97b00dca570#5e05ccb32e2de6797c54768d95e4cc3ba8c8bc5f"><strong style="font-weight: 600;">functional-tests.sh</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -12,8 +12,8 @@ set -o nounset</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC12" class="line" lang="shell"></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC13" class="line" lang="shell"></span>
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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.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="14" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
15
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC15" class="line" lang="shell">nim c <span class="nt" style="color: #000080;">--boundChecks</span>:on <span class="nt" style="color: #000080;">-x</span>:on mosdepth.nim</span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
16
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC16" class="line" lang="shell">nim c <span class="nt" style="color: #000080;">-r</span> tests/funcs.nim</span>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.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="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC15" class="line" lang="shell">nim c <span class="nt" style="color: #000080;">--boundChecks</span>:on <span class="nt" style="color: #000080;">-x</span>:on <span class="nt" style="color: #000080;"><span class="idiff left addition" style="background-color: #c7f0d2;">-d</span></span><span class="idiff addition" style="background-color: #c7f0d2;">:useSysAssert </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">-d</span></span><span class="idiff addition" style="background-color: #c7f0d2;">:useGcAssert </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">--lineDir</span></span><span class="idiff addition" style="background-color: #c7f0d2;">:on </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">--debuginfo</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">--mm</span></span><span class="idiff right addition" style="background-color: #c7f0d2;">:refc </span>mosdepth.nim</span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC16" class="line" lang="shell">nim c <span class="nt" style="color: #000080;"><span class="idiff left addition" style="background-color: #c7f0d2;">-x</span></span><span class="idiff addition" style="background-color: #c7f0d2;">:on </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">--mm</span></span><span class="idiff addition" style="background-color: #c7f0d2;">:refc </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">-d</span></span><span class="idiff addition" style="background-color: #c7f0d2;">:useSysAssert </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">-d</span></span><span class="idiff addition" style="background-color: #c7f0d2;">:useGcAssert </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">--lineDir</span></span><span class="idiff addition" style="background-color: #c7f0d2;">:on </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">--debuginfo</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="nt" style="color: #000080;">-r</span> tests/funcs.nim</span>
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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.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="17" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="shell"><span class="nb" style="color: #0086b3;">set</span> +e</span>
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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.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="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
18
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="shell"><span class="nv" style="color: #008080;">exe</span><span class="o" style="font-weight: 600;">=</span>./mosdepth</span>
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19
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="shell"><span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">=</span>/data/human/NA12878.subset.bam</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="152" style="width: 35px; color: rgba(5,5,6,.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="152" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -152,7 +152,7 @@ rm -f t.*</td>
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152
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<td class="new_line diff-line-num" data-linenumber="152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
152
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC152" class="line" lang="shell"></span>
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<td class="old_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
153
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<td class="new_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
153
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC153" class="line" lang="shell"><span class="c" style="color: #999988; font-style: italic;">#regions and global should not be the same when -b is specified</span></span>
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<td class="old_line diff-line-num" data-linenumber="154" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
154
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<td class="new_line diff-line-num" data-linenumber="154" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
154
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC154" class="line" lang="shell">run regions <span class="nv" style="color: #008080;">$exe</span> t_regions <span class="nt" style="color: #000080;">-n</span> <span class="nt" style="color: #000080;">-b</span> 100 tests/empty-tids.bam </span>
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<td class="old_line diff-line-num old" data-linenumber="155" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
155
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<td class="new_line diff-line-num old" data-linenumber="155" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="shell">assert_equal <span class="si" style="color: #dd1144;">$(</span>diff <span class="nt" style="color: #000080;">-u</span> t_regions.mosdepth.region.dist.txt t_regions.mosdepth.global.dist.txt | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #dd1144;">)</span> 14<span class="idiff left right deletion" style="background-color: #fac5cd;">47</span></span>
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<td class="old_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
155
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC155" class="line" lang="shell">assert_equal <span class="si" style="color: #dd1144;">$(</span>diff <span class="nt" style="color: #000080;">-u</span> t_regions.mosdepth.region.dist.txt t_regions.mosdepth.global.dist.txt | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #dd1144;">)</span> 14<span class="idiff left right addition" style="background-color: #c7f0d2;">36</span></span>
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<td class="old_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
156
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<td class="new_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
156
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> t_regions.<span class="k" style="font-weight: 600;">*</span></span>
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<td class="old_line diff-line-num" data-linenumber="157" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
157
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<td class="new_line diff-line-num" data-linenumber="157" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
157
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="shell"></span>
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<td class="old_line diff-line-num" data-linenumber="158" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
158
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<td class="new_line diff-line-num" data-linenumber="158" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
158
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="shell">run overlappingPairs <span class="nv" style="color: #008080;">$exe</span> t tests/overlapping-pairs.bam</span>
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<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/0ba1c572ff9b8df67fd5a3786aeea97b00dca570#f2a4f454974b64d881d2a470683d1c37fb1aa2bb"><strong style="font-weight: 600;">mosdepth.nim</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="180" style="width: 35px; color: rgba(5,5,6,.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="180" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -180,7 +180,7 @@ iterator regions(bam: hts.Bam, region: region_t, tid: int, targets: seq[hts.Targ</td>
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<td class="old_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
180
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<td class="new_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
180
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC180" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="181" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
181
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<td class="new_line diff-line-num" data-linenumber="181" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
181
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC181" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #990000; font-weight: 600;">bed_line_to_region</span><span class="p">(</span><span class="n" style="color: #333333;">line</span><span class="p">:</span> <span class="kt" style="color: #445588; font-weight: 600;">string</span><span class="p">):</span> <span class="n" style="color: #333333;">region_t</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="old_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
182
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<td class="new_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
182
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC182" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span></span>
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<td class="old_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
183
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<td class="new_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC183" class="line" lang="nim"> <span class="n" style="color: #333333;">cse</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">line</span><span class="p">.</span><span class="n" style="color: #333333;"><span class="idiff left deletion" style="background-color: #fac5cd;">strip</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">().</span></span><span class="n" style="color: #333333;">split</span><span class="p">(</span><span class="sc" style="color: #dd1144;">'</span><span class="se" style="color: #dd1144;">\t</span><span class="sc" style="color: #dd1144;">'</span><span class="p">,</span> <span class="mi" style="color: #009999;">5</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(5,5,6,.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="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
183
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC183" class="line" lang="nim"> <span class="n" style="color: #333333;">cse</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">line</span><span class="p">.</span><span class="n" style="color: #333333;">split</span><span class="p">(</span><span class="sc" style="color: #dd1144;">'</span><span class="se" style="color: #dd1144;">\t</span><span class="sc" style="color: #dd1144;">'</span><span class="p">,</span> <span class="mi" style="color: #009999;">5</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
184
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<td class="new_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
184
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC184" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
185
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<td class="new_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
185
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC185" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">len</span><span class="p">(</span><span class="n" style="color: #333333;">cse</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #009999;">3</span><span class="p">:</span></span>
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186
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<td class="new_line diff-line-num" data-linenumber="186" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
186
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC186" class="line" lang="nim"> <span class="n" style="color: #333333;">stderr</span><span class="p">.</span><span class="n" style="color: #333333;">write_line</span><span class="p">(</span><span class="s" style="color: #dd1144;">"[mosdepth] skipping bad bed line:"</span><span class="p">,</span> <span class="n" style="color: #333333;">line</span><span class="p">.</span><span class="n" style="color: #333333;">strip</span><span class="p">())</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="191" style="width: 35px; color: rgba(5,5,6,.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="191" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -191,7 +191,7 @@ proc bed_line_to_region(line: string): region_t =</td>
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<td class="old_line diff-line-num" data-linenumber="191" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
191
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<td class="new_line diff-line-num" data-linenumber="191" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
191
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC191" class="line" lang="nim"> <span class="n" style="color: #333333;">reg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">region_t</span><span class="p">(</span><span class="n" style="color: #333333;">chrom</span><span class="p">:</span> <span class="n" style="color: #333333;">cse</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333333;">start</span><span class="p">:</span> <span class="n" style="color: #333333;">uint32</span><span class="p">(</span><span class="n" style="color: #333333;">s</span><span class="p">),</span> <span class="n" style="color: #333333;">stop</span><span class="p">:</span> <span class="n" style="color: #333333;">uint32</span><span class="p">(</span><span class="n" style="color: #333333;">e</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(5,5,6,.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="192" style="width: 35px; color: rgba(5,5,6,.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="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC192" class="line" lang="nim"> <span class="n" style="color: #333333;">doAssert</span> <span class="n" style="color: #333333;">s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333333;">e</span><span class="p">,</span> <span class="s" style="color: #dd1144;">"[slivar] ERROR: start > end in bed line:"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333333;">line</span></span>
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<td class="old_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.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="193" style="width: 35px; color: rgba(5,5,6,.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="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC193" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">len</span><span class="p">(</span><span class="n" style="color: #333333;">cse</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #009999;">3</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
194
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<td class="new_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC194" class="line" lang="nim"> <span class="n" style="color: #333333;">reg</span><span class="p">.</span><span class="n" style="color: #333333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">cse</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">3</span><span class="o" style="font-weight: 600;">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(5,5,6,.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="194" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
194
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC194" class="line" lang="nim"> <span class="n" style="color: #333333;">reg</span><span class="p">.</span><span class="n" style="color: #333333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">cse</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">3</span><span class="o" style="font-weight: 600;">]</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">strip</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">()</span></span></span>
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<td class="old_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
195
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<td class="new_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
195
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC195" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">reg</span></span>
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<td class="old_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(5,5,6,.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="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(5,5,6,.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="197" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #990000; font-weight: 600;">region_line_to_region</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333333;">region</span><span class="p">:</span> <span class="kt" style="color: #445588; font-weight: 600;">string</span><span class="p">):</span> <span class="n" style="color: #333333;">region_t</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" style="width: 35px; color: rgba(5,5,6,.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="212" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -212,10 +212,14 @@ proc region_line_to_region*(region: string): region_t =</td>
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<td class="old_line diff-line-num" data-linenumber="212" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
212
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<td class="new_line diff-line-num" data-linenumber="212" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
212
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC212" class="line" lang="nim"> <span class="n" style="color: #333333;">result</span><span class="p">.</span><span class="n" style="color: #333333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">w</span></span>
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<td class="old_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
213
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<td class="new_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
213
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC213" class="line" lang="nim"> <span class="n" style="color: #333333;">inc</span><span class="p">(</span><span class="n" style="color: #333333;">i</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
214
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<td class="new_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
214
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC214" class="line" lang="nim"></span>
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<td class="old_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
215
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<td class="new_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC215" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #990000; font-weight: 600;">get_tid</span><span class="p">(</span><span class="n" style="color: #333333;">tgts</span><span class="p">:</span> <span class="kt" style="color: #445588; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">hts</span><span class="p">.</span><span class="n" style="color: #333333;">Target</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333333;">chrom</span><span class="p">:</span> <span class="kt" style="color: #445588; font-weight: 600;">string</span><span class="p">):</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="old_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(5,5,6,.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="215" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
215
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC215" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #990000; font-weight: 600;">get_tid</span><span class="p">(</span><span class="n" style="color: #333333;">tgts</span><span class="p">:</span> <span class="kt" style="color: #445588; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">hts</span><span class="p">.</span><span class="n" style="color: #333333;">Target</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333333;">chrom</span><span class="p">:</span> <span class="kt" style="color: #445588; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333333;">last_tid</span><span class="p">:</span><span class="k" style="font-weight: 600;">var</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="p">):</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
216
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC216" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">tgts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">last_tid</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">chrom</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
217
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC217" class="line" lang="nim"> <span class="n" style="color: #333333;">last_tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">tgts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">last_tid</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333333;">tid</span></span>
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<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
218
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC218" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">last_tid</span></span>
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<td class="old_line diff-line-num" data-linenumber="216" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
216
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<td class="new_line diff-line-num" data-linenumber="219" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
219
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC219" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">tgts</span><span class="p">:</span></span>
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217
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<td class="new_line diff-line-num" data-linenumber="220" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
220
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC220" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">t</span><span class="p">.</span><span class="n" style="color: #333333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">chrom</span><span class="p">:</span></span>
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218
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<td class="new_line diff-line-num old" data-linenumber="221" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC218" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">t</span><span class="p">.</span><span class="n" style="color: #333333;">tid</span></span>
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<td class="old_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(5,5,6,.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="221" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
221
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC221" class="line" lang="nim"> <span class="n" style="color: #333333;">last_tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">t</span><span class="p">.</span><span class="n" style="color: #333333;">tid</span></span>
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<td class="new_line diff-line-num new" data-linenumber="222" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
222
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC222" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">last_tid</span></span>
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219
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<td class="new_line diff-line-num" data-linenumber="223" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
223
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC223" class="line" lang="nim"></span>
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220
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<td class="new_line diff-line-num" data-linenumber="224" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
224
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC224" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #990000; font-weight: 600;">init</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">coverage_t</span><span class="p">,</span> <span class="n" style="color: #333333;">tlen</span><span class="p">:</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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221
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<td class="new_line diff-line-num" data-linenumber="225" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
225
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC225" class="line" lang="nim"> <span class="sd" style="color: #dd1144;">## try to re-use the array.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="229" style="width: 35px; color: rgba(5,5,6,.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="233" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -229,19 +233,18 @@ proc init(arr: var coverage_t, tlen:int) =</td>
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<td class="old_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
229
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<td class="new_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
233
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC233" class="line" lang="nim"> <span class="n" style="color: #333333;">arr</span><span class="p">.</span><span class="n" style="color: #333333;">set_len</span><span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333333;">tlen</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="230" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
230
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<td class="new_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
234
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC234" class="line" lang="nim"> <span class="n" style="color: #333333;">zeroMem</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="k" style="font-weight: 600;">addr</span><span class="p">,</span> <span class="n" style="color: #333333;">len</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">sizeof</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">))</span></span>
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231
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235
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC235" class="line" lang="nim"></span>
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<td class="new_line diff-line-num old" data-linenumber="236" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC232" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #990000; font-weight: 600;">coverage</span><span class="p">(</span><span class="n" style="color: #333333;">bam</span><span class="p">:</span> <span class="n" style="color: #333333;">hts</span><span class="p">.</span><span class="n" style="color: #333333;">Bam</span><span class="p">,</span> <span class="n" style="color: #333333;">arr</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">coverage_t</span><span class="p">,</span> <span class="n" style="color: #333333;">region</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">region_t</span><span class="p">,</span> <span class="n" style="color: #333333;">mapq</span><span class="p">:</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="p">,</span> <span class="n" style="color: #333333;">min_len</span><span class="p">:</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="p">,</span> <span class="n" style="color: #333333;">max_len</span><span class="p">:</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">=</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="p">.</span><span class="n" style="color: #333333;">high</span><span class="p">,</span> <span class="n" style="color: #333333;">eflag</span><span class="p">:</span> <span class="n" style="color: #333333;">uint16</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #009999;">1796</span><span class="p">,</span> <span class="n" style="color: #333333;">iflag</span><span class="p">:</span><span class="n" style="color: #333333;">uint16</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #009999;">0</span><span class="p">,</span> <span class="n" style="color: #333333;">read_groups</span><span class="p">:</span><span class="kt" style="color: #445588; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">string</span><span class="o" style="font-weight: 600;">]=</span><span class="p">(</span><span class="o" style="font-weight: 600;">@[]</span><span class="p">),</span> <span class="n" style="color: #333333;">fast_mode</span><span class="p">:</span><span class="kt" style="color: #445588; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">=</span><span class="kp" style="font-weight: 600;">false</span><span class="p">):</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="old_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(5,5,6,.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="236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
236
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC236" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #990000; font-weight: 600;">coverage</span><span class="p">(</span><span class="n" style="color: #333333;">bam</span><span class="p">:</span> <span class="n" style="color: #333333;">hts</span><span class="p">.</span><span class="n" style="color: #333333;">Bam</span><span class="p">,</span> <span class="n" style="color: #333333;">arr</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">coverage_t</span><span class="p">,</span> <span class="n" style="color: #333333;">region</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">region_t</span><span class="p">,</span> <span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">targets</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">:</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="kt" style="color: #445588; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">seq</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">[</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">Target</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">]</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;">mapq</span><span class="p">:</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="p">,</span> <span class="n" style="color: #333333;">min_len</span><span class="p">:</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="p">,</span> <span class="n" style="color: #333333;">max_len</span><span class="p">:</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">=</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="p">.</span><span class="n" style="color: #333333;">high</span><span class="p">,</span> <span class="n" style="color: #333333;">eflag</span><span class="p">:</span> <span class="n" style="color: #333333;">uint16</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #009999;">1796</span><span class="p">,</span> <span class="n" style="color: #333333;">iflag</span><span class="p">:</span><span class="n" style="color: #333333;">uint16</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #009999;">0</span><span class="p">,</span> <span class="n" style="color: #333333;">read_groups</span><span class="p">:</span><span class="kt" style="color: #445588; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">string</span><span class="o" style="font-weight: 600;">]=</span><span class="p">(</span><span class="o" style="font-weight: 600;">@[]</span><span class="p">),</span> <span class="n" style="color: #333333;">fast_mode</span><span class="p">:</span><span class="kt" style="color: #445588; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">=</span><span class="kp" style="font-weight: 600;">false</span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">last_tid</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">:</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="k" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">var</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="kt" style="color: #445588; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">int</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">-</span></span><span class="mi" style="color: #009999;"><span class="idiff right addition" style="background-color: #c7f0d2;">1</span></span><span class="p">):</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="old_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
233
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<td class="new_line diff-line-num" data-linenumber="237" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
237
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC237" class="line" lang="nim"> <span class="c" style="color: #999988; font-style: italic;"># depth updates arr in-place and yields the tid for each chrom.</span></span>
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<td class="old_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
234
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<td class="new_line diff-line-num" data-linenumber="238" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
238
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC238" class="line" lang="nim"> <span class="c" style="color: #999988; font-style: italic;"># returns -1 if the chrom is not found in the bam header</span></span>
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<td class="old_line diff-line-num" data-linenumber="235" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
235
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<td class="new_line diff-line-num" data-linenumber="239" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
239
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC239" class="line" lang="nim"> <span class="c" style="color: #999988; font-style: italic;"># returns -2 if the chrom was found in the header, but there was no data for it</span></span>
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<td class="old_line diff-line-num" data-linenumber="236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
236
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<td class="new_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
240
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC240" class="line" lang="nim"> <span class="c" style="color: #999988; font-style: italic;"># otherwise returns the tid.</span></span>
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<td class="old_line diff-line-num" data-linenumber="237" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
237
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<td class="new_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
241
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC241" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span></span>
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<td class="old_line diff-line-num old" data-linenumber="238" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
238
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<td class="new_line diff-line-num old" data-linenumber="242" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC238" class="line" lang="nim"> <span class="n" style="color: #333333;">targets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">bam</span><span class="p">.</span><span class="n" style="color: #333333;">hdr</span><span class="p">.</span><span class="n" style="color: #333333;">targets</span></span>
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<td class="old_line diff-line-num" data-linenumber="239" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
239
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<td class="new_line diff-line-num" data-linenumber="242" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
242
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC242" class="line" lang="nim"> <span class="n" style="color: #333333;">tgt</span><span class="p">:</span> <span class="n" style="color: #333333;">hts</span><span class="p">.</span><span class="n" style="color: #333333;">Target</span></span>
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<td class="old_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
240
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<td class="new_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
243
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC243" class="line" lang="nim"> <span class="n" style="color: #333333;">mate</span><span class="p">:</span> <span class="n" style="color: #333333;">Record</span></span>
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<td class="old_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
241
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<td class="new_line diff-line-num" data-linenumber="244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
244
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC244" class="line" lang="nim"> <span class="n" style="color: #333333;">seen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">newTable</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333333;">Record</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="242" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
242
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<td class="new_line diff-line-num" data-linenumber="245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
245
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC245" class="line" lang="nim"> <span class="n" style="color: #333333;">has_read_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">read_groups</span><span class="p">.</span><span class="n" style="color: #333333;">len</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #009999;">0</span></span>
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<td class="old_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
243
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<td class="new_line diff-line-num" data-linenumber="246" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
246
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC246" class="line" lang="nim"></span>
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<td class="old_line diff-line-num old" data-linenumber="244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
244
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<td class="new_line diff-line-num old" data-linenumber="247" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC244" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">region</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span> <span class="n" style="color: #333333;">get_tid</span><span class="p">(</span><span class="n" style="color: #333333;">targets</span><span class="p">,</span> <span class="n" style="color: #333333;">region</span><span class="p">.</span><span class="n" style="color: #333333;">chrom</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span></span>
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<td class="old_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(5,5,6,.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="247" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
247
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC247" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">region</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span> <span class="n" style="color: #333333;">get_tid</span><span class="p">(</span><span class="n" style="color: #333333;">targets</span><span class="p">,</span> <span class="n" style="color: #333333;">region</span><span class="p">.</span><span class="n" style="color: #333333;">chrom</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">last_tid</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span></span>
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<td class="old_line diff-line-num" data-linenumber="245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
245
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<td class="new_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
248
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC248" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">tid</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="246" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
246
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<td class="new_line diff-line-num" data-linenumber="249" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
249
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC249" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span></span>
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<td class="old_line diff-line-num" data-linenumber="247" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
247
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<td class="new_line diff-line-num" data-linenumber="250" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
250
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC250" class="line" lang="nim"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="335" style="width: 35px; color: rgba(5,5,6,.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="338" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -335,8 +338,7 @@ proc bed_to_table(bed: string): TableRef[string, seq[region_t]] =</td>
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<td class="old_line diff-line-num" data-linenumber="335" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
335
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<td class="new_line diff-line-num" data-linenumber="338" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
338
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="old_line diff-line-num" data-linenumber="336" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
336
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<td class="new_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
339
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC339" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">bed_line_to_region</span><span class="p">(</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333333;">kstr</span><span class="p">.</span><span class="n" style="color: #333333;">s</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="337" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
337
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<td class="new_line diff-line-num" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
340
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC340" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">v</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="old_line diff-line-num old" data-linenumber="338" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
338
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<td class="new_line diff-line-num old" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333333;">bed_regions</span><span class="p">.</span><span class="n" style="color: #333333;">hasKeyOrPut</span><span class="p">(</span><span class="n" style="color: #333333;">v</span><span class="p">.</span><span class="n" style="color: #333333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">region_t</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 old" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
339
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<td class="new_line diff-line-num old" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC339" class="line" lang="nim"> <span class="n" style="color: #333333;">bed_regions</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">v</span><span class="p">.</span><span class="n" style="color: #333333;">chrom</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333333;">add</span><span class="p">(</span><span class="n" style="color: #333333;">v</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.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="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
341
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC341" class="line" lang="nim"> <span class="n" style="color: #333333;">bed_regions</span><span class="p">.</span><span class="n" style="color: #333333;">mgetOrPut</span><span class="p">(</span><span class="n" style="color: #333333;">v</span><span class="p">.</span><span class="n" style="color: #333333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">region_t</span><span class="o" style="font-weight: 600;">]</span><span class="p">()).</span><span class="n" style="color: #333333;">add</span><span class="p">(</span><span class="n" style="color: #333333;">v</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
340
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<td class="new_line diff-line-num" data-linenumber="342" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
342
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC342" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
341
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<td class="new_line diff-line-num" data-linenumber="343" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
343
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC343" class="line" lang="nim"> <span class="c" style="color: #999988; font-style: italic;"># since it is read into mem, can also well sort.</span></span>
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<td class="old_line diff-line-num" data-linenumber="342" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
342
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<td class="new_line diff-line-num" data-linenumber="344" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
344
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC344" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333333;">ivs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">bed_regions</span><span class="p">.</span><span class="n" style="color: #333333;">mpairs</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="414" style="width: 35px; color: rgba(5,5,6,.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="416" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -414,7 +416,7 @@ proc write_distribution(chrom: string, d: var seq[int64], fh:File) =</td>
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<td class="old_line diff-line-num" data-linenumber="414" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
414
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<td class="new_line diff-line-num" data-linenumber="416" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
416
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC416" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">irev</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #009999;">300</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">v</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">0</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="old_line diff-line-num" data-linenumber="415" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
415
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<td class="new_line diff-line-num" data-linenumber="417" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
417
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC417" class="line" lang="nim"> <span class="n" style="color: #333333;">cum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="kt" style="color: #445588; font-weight: 600;">float64</span><span class="p">(</span><span class="n" style="color: #333333;">v</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="kt" style="color: #445588; font-weight: 600;">float64</span><span class="p">(</span><span class="n" style="color: #333333;">sum</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="416" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
416
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<td class="new_line diff-line-num" data-linenumber="418" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
418
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC418" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">cum</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #009999;">8e-5</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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417
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<td class="new_line diff-line-num old" data-linenumber="419" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC417" class="line" lang="nim"> <span class="n" style="color: #333333;">fh</span><span class="p">.</span><span class="n" style="color: #333333;">write_line</span><span class="p">(</span><span class="n" style="color: #333333;">chrom</span><span class="p">,</span> <span class="s" style="color: #dd1144;">"</span><span class="se" style="color: #dd1144;">\t</span><span class="s" style="color: #dd1144;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;">$</span></span><span class="n" style="color: #333333;">irev</span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">&</span></span> <span class="s" style="color: #dd1144;">"</span><span class="se" style="color: #dd1144;">\t</span><span class="s" style="color: #dd1144;">"</span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">&</span></span> <span class="n" style="color: #333333;">su</span><span class="p">.</span><span class="n" style="color: #333333;">format_float</span><span class="p">(</span><span class="n" style="color: #333333;">cum</span><span class="p">,</span> <span class="n" style="color: #333333;">ffDecimal</span><span class="p">,</span> <span class="n" style="color: #333333;">precision</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">precision</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
419
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC419" class="line" lang="nim"> <span class="n" style="color: #333333;">fh</span><span class="p">.</span><span class="n" style="color: #333333;">write_line</span><span class="p">(</span><span class="n" style="color: #333333;">chrom</span><span class="p">,</span> <span class="s" style="color: #dd1144;">"</span><span class="se" style="color: #dd1144;">\t</span><span class="s" style="color: #dd1144;">"</span><span class="p">,</span> <span class="n" style="color: #333333;">irev</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span> <span class="s" style="color: #dd1144;">"</span><span class="se" style="color: #dd1144;">\t</span><span class="s" style="color: #dd1144;">"</span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">,</span></span> <span class="n" style="color: #333333;">su</span><span class="p">.</span><span class="n" style="color: #333333;">format_float</span><span class="p">(</span><span class="n" style="color: #333333;">cum</span><span class="p">,</span> <span class="n" style="color: #333333;">ffDecimal</span><span class="p">,</span> <span class="n" style="color: #333333;">precision</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">precision</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="418" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
418
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<td class="new_line diff-line-num" data-linenumber="420" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
420
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC420" class="line" lang="nim"> <span class="c" style="color: #999988; font-style: italic;"># reverse it back because we use to update the full genome</span></span>
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419
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<td class="new_line diff-line-num" data-linenumber="421" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
421
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC421" class="line" lang="nim"> <span class="n" style="color: #333333;">reverse</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="p">)</span></span>
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422
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC422" class="line" lang="nim"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="456" style="width: 35px; color: rgba(5,5,6,.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="458" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -456,8 +458,8 @@ proc sum_into(afrom: seq[int64], ato: var seq[int64]) =</td>
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456
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<td class="new_line diff-line-num" data-linenumber="458" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
458
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC458" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">b</span><span class="p">..</span><span class="n" style="color: #333333;">ato</span><span class="p">.</span><span class="n" style="color: #333333;">high</span><span class="p">:</span></span>
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457
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<td class="new_line diff-line-num" data-linenumber="459" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
459
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC459" class="line" lang="nim"> <span class="n" style="color: #333333;">ato</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span></span>
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458
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460
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC460" class="line" lang="nim"></span>
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459
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<td class="new_line diff-line-num old" data-linenumber="461" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC459" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="mf" style="color: #009999;"><span class="idiff left deletion" style="background-color: #fac5cd;">0</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">..</span></span><span class="n" style="color: #333333;">afrom</span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333333;"><span class="idiff right deletion" style="background-color: #fac5cd;">high</span></span><span class="p">:</span></span>
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460
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<td class="new_line diff-line-num old" data-linenumber="461" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC460" class="line" lang="nim"> <span class="n" style="color: #333333;">ato</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333333;"><span class="idiff left deletion" style="background-color: #fac5cd;">afrom</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="461" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
461
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC461" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">i</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">d</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">afrom</span><span class="p">:</span></span>
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462
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC462" class="line" lang="nim"> <span class="n" style="color: #333333;">ato</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">d</span></span></span>
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461
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463
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC463" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="462" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
462
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<td class="new_line diff-line-num" data-linenumber="464" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
464
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC464" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #990000; font-weight: 600;">get_quantize_args</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333333;">qa</span><span class="p">:</span> <span class="kt" style="color: #445588; font-weight: 600;">string</span><span class="p">)</span> <span class="p">:</span> <span class="kt" style="color: #445588; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span></span>
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463
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<td class="new_line diff-line-num" data-linenumber="465" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
465
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC465" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">qa</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #dd1144;">"nil"</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="502" style="width: 35px; color: rgba(5,5,6,.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="504" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -502,7 +504,8 @@ proc write_thresholds(fh:BGZI, tid:int, arr:var coverage_t, thresholds:seq[int],</td>
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502
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<td class="new_line diff-line-num" data-linenumber="504" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
504
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC504" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span></span>
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503
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505
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC505" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="504" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
504
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<td class="new_line diff-line-num" data-linenumber="506" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
506
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC506" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333333;">len</span><span class="p">(</span><span class="n" style="color: #333333;">thresholds</span><span class="p">))</span></span>
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505
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<td class="new_line diff-line-num old" data-linenumber="507" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC505" class="line" lang="nim"> <span class="n" style="color: #333333;">shallow</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="507" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
507
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC507" class="line" lang="nim"> <span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333333;">NimMajor</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #009999;">2</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="508" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
508
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC508" class="line" lang="nim"> <span class="n" style="color: #333333;">shallow</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="p">)</span></span>
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506
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<td class="new_line diff-line-num" data-linenumber="509" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
509
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC509" class="line" lang="nim"></span>
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507
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<td class="new_line diff-line-num" data-linenumber="510" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
510
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC510" class="line" lang="nim"> <span class="c" style="color: #999988; font-style: italic;"># iterate over the region and count bases >= request cutoffs.</span></span>
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508
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<td class="new_line diff-line-num" data-linenumber="511" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
511
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC511" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">start</span><span class="p">..</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333333;">stop</span><span class="o" style="font-weight: 600;">]</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="584" style="width: 35px; color: rgba(5,5,6,.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="587" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -584,15 +587,16 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, min_len: int, max_len: int,</td>
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584
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<td class="new_line diff-line-num" data-linenumber="587" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
587
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC587" class="line" lang="nim"> <span class="n" style="color: #333333;">global_region_stat</span><span class="p">.</span><span class="n" style="color: #333333;">clear</span><span class="p">()</span></span>
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585
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<td class="new_line diff-line-num" data-linenumber="588" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
588
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC588" class="line" lang="nim"> <span class="n" style="color: #333333;">global_stat</span><span class="p">.</span><span class="n" style="color: #333333;">clear</span><span class="p">()</span></span>
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586
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<td class="new_line diff-line-num" data-linenumber="589" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
589
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC589" class="line" lang="nim"></span>
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<td class="old_line diff-line-num old" data-linenumber="587" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
587
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<td class="new_line diff-line-num old" data-linenumber="590" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC587" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">region_distribution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="mi" style="color: #009999;"><span class="idiff left right deletion" style="background-color: #fac5cd;">1000</span></span><span class="p">)</span></span>
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588
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<td class="new_line diff-line-num old" data-linenumber="590" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC588" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">global_distribution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="mi" style="color: #009999;"><span class="idiff left right deletion" style="background-color: #fac5cd;">1000</span></span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="589" style="width: 35px; color: rgba(5,5,6,.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="590" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
590
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC590" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">region_distribution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="mi" style="color: #009999;"><span class="idiff left right addition" style="background-color: #c7f0d2;">512</span></span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="589" style="width: 35px; color: rgba(5,5,6,.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="591" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
591
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC591" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">global_distribution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="mi" style="color: #009999;"><span class="idiff left right addition" style="background-color: #c7f0d2;">512</span></span><span class="p">)</span></span>
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589
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<td class="new_line diff-line-num" data-linenumber="592" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
592
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC592" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="590" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
590
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<td class="new_line diff-line-num" data-linenumber="593" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
593
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC593" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #dd1144;">"--read-groups"</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #dd1144;">"nil"</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="591" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
591
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<td class="new_line diff-line-num" data-linenumber="594" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
594
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC594" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #dd1144;">"--read-groups"</span><span class="o" style="font-weight: 600;">]</span><span class="p">).</span><span class="n" style="color: #333333;">split</span><span class="p">(</span><span class="sc" style="color: #dd1144;">','</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="592" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
592
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<td class="new_line diff-line-num" data-linenumber="595" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
595
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC595" class="line" lang="nim"> <span class="n" style="color: #333333;">read_groups</span><span class="p">.</span><span class="n" style="color: #333333;">add</span><span class="p">(</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333333;">r</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="593" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
593
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<td class="new_line diff-line-num" data-linenumber="596" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
596
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC596" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">levels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">get_min_levels</span><span class="p">(</span><span class="n" style="color: #333333;">targets</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="594" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
594
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<td class="new_line diff-line-num" data-linenumber="597" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
597
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC597" class="line" lang="nim"></span>
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<td class="old_line diff-line-num old" data-linenumber="595" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
595
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<td class="new_line diff-line-num old" data-linenumber="598" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC595" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">chrom_region_distribution</span><span class="p">,</span> <span class="n" style="color: #333333;">chrom_global_distribution</span><span class="p">:</span> <span class="kt" style="color: #445588; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="596" style="width: 35px; color: rgba(5,5,6,.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="598" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
598
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC598" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">chrom_region_distribution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">newSeq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333333;">region_distribution</span><span class="p">.</span><span class="n" style="color: #333333;">len</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="596" style="width: 35px; color: rgba(5,5,6,.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="599" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
599
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC599" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">chrom_global_distribution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">newSeq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333333;">global_distribution</span><span class="p">.</span><span class="n" style="color: #333333;">len</span><span class="p">)</span></span>
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596
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<td class="new_line diff-line-num" data-linenumber="600" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
600
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC600" class="line" lang="nim"></span>
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597
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<td class="new_line diff-line-num" data-linenumber="601" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
601
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC601" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">skip_per_base</span><span class="p">:</span></span>
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598
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<td class="new_line diff-line-num" data-linenumber="602" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
602
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC602" class="line" lang="nim"> <span class="c" style="color: #999988; font-style: italic;"># can't use set-threads when indexing on the fly so this must</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="627" style="width: 35px; color: rgba(5,5,6,.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="631" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -627,19 +631,26 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, min_len: int, max_len: int,</td>
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627
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631
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC631" class="line" lang="nim"> <span class="n" style="color: #333333;">window</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">uint32</span><span class="p">(</span><span class="n" style="color: #333333;">S</span><span class="p">.</span><span class="n" style="color: #333333;">parse_int</span><span class="p">(</span><span class="n" style="color: #333333;">region</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="628" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
628
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<td class="new_line diff-line-num" data-linenumber="632" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
632
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC632" class="line" lang="nim"> <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="629" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
629
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<td class="new_line diff-line-num" data-linenumber="633" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
633
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC633" class="line" lang="nim"> <span class="n" style="color: #333333;">bed_regions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">bed_to_table</span><span class="p">(</span><span class="n" style="color: #333333;">region</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="630" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
630
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<td class="new_line diff-line-num old" data-linenumber="634" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC630" class="line" lang="nim"> <span class="n" style="color: #333333;">shallow</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="631" style="width: 35px; color: rgba(5,5,6,.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="634" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
634
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC634" class="line" lang="nim"> <span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333333;">NimMajor</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #009999;">2</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="631" style="width: 35px; color: rgba(5,5,6,.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="635" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
635
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC635" class="line" lang="nim"> <span class="n" style="color: #333333;">shallow</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="p">)</span></span>
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631
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<td class="new_line diff-line-num" data-linenumber="636" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
636
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC636" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="632" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
632
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<td class="new_line diff-line-num" data-linenumber="637" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
637
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC637" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">cs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">initCountStat</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">uint32</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333333;">size</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">use_median</span><span class="p">:</span> <span class="mi" style="color: #009999;">65536</span> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="mi" style="color: #009999;">0</span><span class="p">)</span></span>
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633
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<td class="new_line diff-line-num" data-linenumber="638" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
638
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC638" class="line" lang="nim"></span>
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<td class="old_line diff-line-num new" data-linenumber="634" style="width: 35px; color: rgba(5,5,6,.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="639" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
639
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC639" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">ii</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="640" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
640
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC640" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">last_tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="641" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
641
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC641" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="634" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
634
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<td class="new_line diff-line-num" data-linenumber="642" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
642
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC642" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">target</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">sub_targets</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="635" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
635
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<td class="new_line diff-line-num old" data-linenumber="643" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC635" class="line" lang="nim"> <span class="n" style="color: #333333;">chrom_global_distribution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #445588; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="mi" style="color: #009999;">1000</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="643" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
643
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC643" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">ii</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #009999;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">ii</span> <span class="ow" style="font-weight: 600;">mod</span> <span class="mi" style="color: #009999;">100_000</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">0</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="644" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
644
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC644" class="line" lang="nim"> <span class="n" style="color: #333333;">stderr</span><span class="p">.</span><span class="n" style="color: #333333;">write_line</span><span class="p">(</span><span class="s" style="color: #dd1144;">"[mosdepth] on contig:"</span><span class="p">,</span> <span class="n" style="color: #333333;">ii</span><span class="p">,</span> <span class="s" style="color: #dd1144;">". percent of contigs completed:"</span><span class="p">,</span> <span class="n" style="color: #333333;">su</span><span class="p">.</span><span class="n" style="color: #333333;">format_float</span><span class="p">(</span><span class="mi" style="color: #009999;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">ii</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">sub_targets</span><span class="p">.</span><span class="n" style="color: #333333;">len</span><span class="p">,</span> <span class="n" style="color: #333333;">ffDecimal</span><span class="p">,</span> <span class="n" style="color: #333333;">precision</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #009999;">2</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="645" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
645
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC645" class="line" lang="nim"> <span class="n" style="color: #333333;">ii</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #009999;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="646" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
646
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC646" class="line" lang="nim"> <span class="n" style="color: #333333;">zeroMem</span><span class="p">(</span><span class="n" style="color: #333333;">chrom_global_distribution</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="k" style="font-weight: 600;">addr</span><span class="p">,</span> <span class="n" style="color: #333333;">len</span><span class="p">(</span><span class="n" style="color: #333333;">chrom_global_distribution</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">sizeof</span><span class="p">(</span><span class="n" style="color: #333333;">chrom_global_distribution</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</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="636" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
636
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<td class="new_line diff-line-num" data-linenumber="647" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
647
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC647" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">region</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #dd1144;">""</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="637" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
637
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<td class="new_line diff-line-num old" data-linenumber="648" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC637" class="line" lang="nim"> <span class="n" style="color: #333333;">chrom_region_distribution</span><span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">=</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">new_seq</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[</span></span><span class="kt" style="color: #445588; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">int64</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">]</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="mi" style="color: #009999;"><span class="idiff right deletion" style="background-color: #fac5cd;">1000</span></span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="638" style="width: 35px; color: rgba(5,5,6,.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="648" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
648
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC648" class="line" lang="nim"> <span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">zeroMem</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;">chrom_region_distribution</span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">[</span></span><span class="mi" style="color: #009999;"><span class="idiff addition" style="background-color: #c7f0d2;">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">]</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="k" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">addr</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">len</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">chrom_region_distribution</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">)</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">*</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">sizeof</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">chrom_region_distribution</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">[</span></span><span class="mi" style="color: #009999;"><span class="idiff addition" style="background-color: #c7f0d2;">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">]</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span>)</span></span>
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<td class="old_line diff-line-num" data-linenumber="638" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
638
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<td class="new_line diff-line-num" data-linenumber="649" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
649
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC649" class="line" lang="nim"> <span class="c" style="color: #999988; font-style: italic;"># if we can skip per base and there's no regions from this chrom we can avoid coverage calc.</span></span>
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<td class="old_line diff-line-num" data-linenumber="639" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
639
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<td class="new_line diff-line-num" data-linenumber="650" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
650
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC650" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">skip_per_base</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">thresholds</span><span class="p">.</span><span class="n" style="color: #333333;">len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">quantize</span><span class="p">.</span><span class="n" style="color: #333333;">len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">bed_regions</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">bed_regions</span><span class="p">.</span><span class="n" style="color: #333333;">contains</span><span class="p">(</span><span class="n" style="color: #333333;">target</span><span class="p">.</span><span class="n" style="color: #333333;">name</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="640" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
640
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<td class="new_line diff-line-num" data-linenumber="651" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
651
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC651" class="line" lang="nim"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="old_line diff-line-num" data-linenumber="641" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
641
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<td class="new_line diff-line-num" data-linenumber="652" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
652
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC652" class="line" lang="nim"> <span class="n" style="color: #333333;">rchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">region_t</span><span class="p">(</span><span class="n" style="color: #333333;">chrom</span><span class="p">:</span> <span class="n" style="color: #333333;">target</span><span class="p">.</span><span class="n" style="color: #333333;">name</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="642" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
642
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<td class="new_line diff-line-num old" data-linenumber="653" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC642" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">coverage</span><span class="p">(</span><span class="n" style="color: #333333;">bam</span><span class="p">,</span> <span class="n" style="color: #333333;">arr</span><span class="p">,</span> <span class="n" style="color: #333333;">rchrom</span><span class="p">,</span> <span class="n" style="color: #333333;">mapq</span><span class="p">,</span> <span class="n" style="color: #333333;">min_len</span><span class="p">,</span> <span class="n" style="color: #333333;">max_len</span><span class="p">,</span> <span class="n" style="color: #333333;">eflag</span><span class="p">,</span> <span class="n" style="color: #333333;">iflag</span><span class="p">,</span> <span class="n" style="color: #333333;">read_groups</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">read_groups</span><span class="p">,</span> <span class="n" style="color: #333333;">fast_mode</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">fast_mode</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="643" style="width: 35px; color: rgba(5,5,6,.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="653" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
653
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC653" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">coverage</span><span class="p">(</span><span class="n" style="color: #333333;">bam</span><span class="p">,</span> <span class="n" style="color: #333333;">arr</span><span class="p">,</span> <span class="n" style="color: #333333;">rchrom</span><span class="p">,</span> <span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">targets</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;">mapq</span><span class="p">,</span> <span class="n" style="color: #333333;">min_len</span><span class="p">,</span> <span class="n" style="color: #333333;">max_len</span><span class="p">,</span> <span class="n" style="color: #333333;">eflag</span><span class="p">,</span> <span class="n" style="color: #333333;">iflag</span><span class="p">,</span> <span class="n" style="color: #333333;">read_groups</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">read_groups</span><span class="p">,</span> <span class="n" style="color: #333333;">fast_mode</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">fast_mode</span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">last_tid</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">last_tid</span></span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="643" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
643
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<td class="new_line diff-line-num" data-linenumber="654" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
654
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC654" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">tid</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span> <span class="c" style="color: #999988; font-style: italic;"># -1 means that chrom is not even in the bam</span></span>
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644
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<td class="new_line diff-line-num" data-linenumber="655" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
655
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC655" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">tid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">2</span><span class="p">:</span> <span class="c" style="color: #999988; font-style: italic;"># -2 means there were no reads in the bam</span></span>
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<td class="old_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
645
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<td class="new_line diff-line-num" data-linenumber="656" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
656
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC656" class="line" lang="nim"> <span class="n" style="color: #333333;">arr</span><span class="p">.</span><span class="n" style="color: #333333;">to_coverage</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="667" style="width: 35px; color: rgba(5,5,6,.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="678" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -667,6 +678,7 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, min_len: int, max_len: int,</td>
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667
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<td class="new_line diff-line-num" data-linenumber="678" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
678
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC678" class="line" lang="nim"> <span class="n" style="color: #333333;">chrom_region_distribution</span><span class="p">.</span><span class="n" style="color: #333333;">inc</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="p">,</span> <span class="n" style="color: #333333;">r</span><span class="p">.</span><span class="n" style="color: #333333;">start</span><span class="p">,</span> <span class="n" style="color: #333333;">r</span><span class="p">.</span><span class="n" style="color: #333333;">stop</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="668" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
668
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<td class="new_line diff-line-num" data-linenumber="679" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
679
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC679" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="669" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
669
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<td class="new_line diff-line-num" data-linenumber="680" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
680
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC680" class="line" lang="nim"> <span class="n" style="color: #333333;">write_thresholds</span><span class="p">(</span><span class="n" style="color: #333333;">fthresholds</span><span class="p">,</span> <span class="n" style="color: #333333;">tid</span><span class="p">,</span> <span class="n" style="color: #333333;">arr</span><span class="p">,</span> <span class="n" style="color: #333333;">thresholds</span><span class="p">,</span> <span class="n" style="color: #333333;">r</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="670" style="width: 35px; color: rgba(5,5,6,.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="681" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
681
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC681" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="670" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
670
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<td class="new_line diff-line-num" data-linenumber="682" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
682
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC682" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">tid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">2</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="671" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
671
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<td class="new_line diff-line-num" data-linenumber="683" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
683
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC683" class="line" lang="nim"> <span class="n" style="color: #333333;">chrom_global_distribution</span><span class="p">.</span><span class="n" style="color: #333333;">inc</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="p">,</span> <span class="n" style="color: #333333;">uint32</span><span class="p">(</span><span class="mi" style="color: #009999;">0</span><span class="p">),</span> <span class="n" style="color: #333333;">uint32</span><span class="p">(</span><span class="n" style="color: #333333;">len</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #009999;">1</span><span class="p">))</span></span>
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672
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<td class="new_line diff-line-num" data-linenumber="684" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
684
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC684" class="line" lang="nim"> <span class="n" style="color: #333333;">chrom_stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">newDepthStat</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="mf" style="color: #009999;">0</span><span class="p">..</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333333;">len</span><span class="p">(</span><span class="n" style="color: #333333;">arr</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="750" style="width: 35px; color: rgba(5,5,6,.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="762" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -750,6 +762,7 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, min_len: int, max_len: int,</td>
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<td class="old_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
750
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<td class="new_line diff-line-num" data-linenumber="762" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
762
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC762" class="line" lang="nim"> <span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333333;">defined</span><span class="p">(</span><span class="n" style="color: #333333;">d4</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
751
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<td class="new_line diff-line-num" data-linenumber="763" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
763
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC763" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">use_d4</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
752
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<td class="new_line diff-line-num" data-linenumber="764" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
764
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC764" class="line" lang="nim"> <span class="n" style="color: #333333;">fd4</span><span class="p">.</span><span class="n" style="color: #333333;">close</span></span>
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<td class="old_line diff-line-num new" data-linenumber="753" style="width: 35px; color: rgba(5,5,6,.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="765" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
765
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC765" class="line" lang="nim"> <span class="n" style="color: #333333;">doAssert</span> <span class="n" style="color: #333333;">index_build_sfi</span><span class="p">(</span><span class="n" style="color: #333333;">prefix</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #dd1144;">".per-base.d4"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="753" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
753
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<td class="new_line diff-line-num" data-linenumber="766" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
766
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC766" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="754" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
754
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<td class="new_line diff-line-num" data-linenumber="767" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
767
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC767" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">fbase</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">close</span><span class="p">(</span><span class="n" style="color: #333333;">fbase</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #009999;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
755
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<td class="new_line diff-line-num" data-linenumber="768" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
768
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC768" class="line" lang="nim"> <span class="n" style="color: #333333;">stderr</span><span class="p">.</span><span class="n" style="color: #333333;">write_line</span><span class="p">(</span><span class="s" style="color: #dd1144;">"[mosdepth] error writing per-base file</span><span class="se" style="color: #dd1144;">\n</span><span class="s" style="color: #dd1144;">"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="795" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -782,7 +795,7 @@ when(isMainModule):</td>
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<td class="old_line diff-line-num" data-linenumber="782" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
782
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<td class="new_line diff-line-num" data-linenumber="795" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
795
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC795" class="line" lang="nim"> <span class="k" style="font-weight: 600;">when</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">defined</span><span class="p">(</span><span class="n" style="color: #333333;">release</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">defined</span><span class="p">(</span><span class="n" style="color: #333333;">lto</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="783" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
783
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<td class="new_line diff-line-num" data-linenumber="796" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
796
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC796" class="line" lang="nim"> <span class="n" style="color: #333333;">stderr</span><span class="p">.</span><span class="n" style="color: #333333;">write_line</span> <span class="s" style="color: #dd1144;">"[mosdepth] WARNING: built in debug mode; will be slow"</span></span>
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<td class="old_line diff-line-num" data-linenumber="784" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
784
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<td class="new_line diff-line-num" data-linenumber="797" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
797
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC797" class="line" lang="nim"></span>
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<td class="old_line diff-line-num old" data-linenumber="785" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
785
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<td class="new_line diff-line-num old" data-linenumber="798" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC785" class="line" lang="nim"> <span class="k" style="font-weight: 600;">let</span> <span class="n" style="color: #333333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #dd1144;">"mosdepth 0.3.<span class="idiff left right deletion" style="background-color: #fac5cd;">6</span>"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(5,5,6,.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="798" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
798
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC798" class="line" lang="nim"> <span class="k" style="font-weight: 600;">let</span> <span class="n" style="color: #333333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #dd1144;">"mosdepth 0.3.<span class="idiff left right addition" style="background-color: #c7f0d2;">10</span>"</span></span>
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<td class="old_line diff-line-num" data-linenumber="786" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
786
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<td class="new_line diff-line-num" data-linenumber="799" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
799
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC799" class="line" lang="nim"> <span class="k" style="font-weight: 600;">let</span> <span class="n" style="color: #333333;">env_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">getEnv</span><span class="p">(</span><span class="s" style="color: #dd1144;">"REF_PATH"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="787" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
787
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<td class="new_line diff-line-num" data-linenumber="800" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
800
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC800" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333333;">doc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">format</span><span class="p">(</span><span class="s" style="color: #dd1144;">"""</span></span>
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<td class="old_line diff-line-num" data-linenumber="788" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
788
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<td class="new_line diff-line-num" data-linenumber="801" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
801
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC801" class="line" lang="nim"><span class="s" style="color: #dd1144;"> </span><span class="si" style="color: #dd1144;">$version</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="791" style="width: 35px; color: rgba(5,5,6,.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="804" style="width: 35px; color: rgba(5,5,6,.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(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -791,7 +804,7 @@ when(isMainModule):</td>
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<td class="old_line diff-line-num" data-linenumber="791" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
791
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<td class="new_line diff-line-num" data-linenumber="804" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
804
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC804" class="line" lang="nim"></span>
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<td class="old_line diff-line-num" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
792
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<td class="new_line diff-line-num" data-linenumber="805" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
805
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC805" class="line" lang="nim"><span class="s" style="color: #dd1144;">Arguments:</span></span>
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<td class="old_line diff-line-num" data-linenumber="793" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
793
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<td class="new_line diff-line-num" data-linenumber="806" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
806
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC806" class="line" lang="nim"></span>
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<td class="old_line diff-line-num old" data-linenumber="794" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
794
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<td class="new_line diff-line-num old" data-linenumber="807" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC794" class="line" lang="nim"><span class="s" style="color: #dd1144;"> <prefix> outputs: `{prefix}.mosdepth.dist.txt`</span></span>
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<td class="old_line diff-line-num new" data-linenumber="795" style="width: 35px; color: rgba(5,5,6,.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="807" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
807
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC807" class="line" lang="nim"><span class="s" style="color: #dd1144;"> <prefix> outputs: `{prefix}.mosdepth.<span class="idiff left right addition" style="background-color: #c7f0d2;">global.</span>dist.txt`</span></span>
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<td class="old_line diff-line-num" data-linenumber="795" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
795
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<td class="new_line diff-line-num" data-linenumber="808" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
808
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC808" class="line" lang="nim"><span class="s" style="color: #dd1144;"> `{prefix}.mosdepth.summary.txt`</span></span>
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<td class="old_line diff-line-num" data-linenumber="796" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
796
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<td class="new_line diff-line-num" data-linenumber="809" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
809
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC809" class="line" lang="nim"><span class="s" style="color: #dd1144;"> `{prefix}.per-base.bed.gz` (unless -n/--no-per-base is specified)</span></span>
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<td class="old_line diff-line-num" data-linenumber="797" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
797
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<td class="new_line diff-line-num" data-linenumber="810" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
810
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC810" class="line" lang="nim"><span class="s" style="color: #dd1144;"> `{prefix}.regions.bed.gz` (if --by is specified)</span></span>
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<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/0ba1c572ff9b8df67fd5a3786aeea97b00dca570#a99b7e9ffb6c06b4832f1c7ce8d8dbbf023f7502"><strong style="font-weight: 600;">mosdepth.nimble</strong></a>
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1
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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC1" class="line" lang="plaintext"># Package</span>
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2
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC2" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC3" class="line" lang="plaintext">version = "0.3.<span class="idiff left right deletion" style="background-color: #fac5cd;">6</span>"</span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC3" class="line" lang="plaintext">version = "0.3.<span class="idiff left right addition" style="background-color: #c7f0d2;">10</span>"</span>
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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC4" class="line" lang="plaintext">author = "Brent Pedersen"</span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC5" class="line" lang="plaintext">description = "fast depth"</span>
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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC6" class="line" lang="plaintext">license = "MIT"</span>
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7
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC7" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
8
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC8" class="line" lang="plaintext"># Dependencies</span>
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9
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9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC9" class="line" lang="plaintext"></span>
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10
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<td class="new_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.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: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC10" class="line" lang="plaintext">requires "hts >= 0.3.22", "docopt == 0.7.<span class="idiff left deletion" style="background-color: #fac5cd;">0</span>", "nim >= 1.0.0", "https://github.com/brentp/d4-nim >= 0.0.<span class="idiff right deletion" style="background-color: #fac5cd;">3</span>"</span>
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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.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="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC10" class="line" lang="plaintext">requires "hts >= 0.3.22", "docopt == 0.7.<span class="idiff left addition" style="background-color: #c7f0d2;">1</span>", "nim >= 1.0.0", "https://github.com/brentp/d4-nim >= 0.0.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>"</span>
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11
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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
11
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC11" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
12
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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
12
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC12" class="line" lang="plaintext">bin = @["mosdepth"]</span>
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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13
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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","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="LC13" class="line" lang="plaintext">skipDirs = @["tests"]</span>
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