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Emmanuel Arias pushed to branch master at <a href="https://salsa.debian.org/med-team/python-pybedtools">Debian Med / python-pybedtools</a>
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Commits:
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/python-pybedtools/-/commit/5bbdbb4354a20e4d4c7c172163f01f40470816dc">5bbdbb43</a></strong>
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<span> by Emmanuel Arias </span> <i> at 2024-12-24T19:26:33-03:00 </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;'>d/patches/fix-doctest-imports.py: Add patch from upstream to use
explicit namespace in docstrings of long_range_interaction file (Closes:
#1090283).
</pre>
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/python-pybedtools/-/commit/12be1cca9a242dd97e15deed361a67d06788e92c">12be1cca</a></strong>
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<span> by Emmanuel Arias </span> <i> at 2024-12-24T19:26:54-03:00 </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;'>prepare for upload
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3 changed files:
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debian/changelog
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debian/patches/fix-doctest-imports.py
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Changes:
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<a href="https://salsa.debian.org/med-team/python-pybedtools/-/compare/a63b21265eb3609c14e213d8ef721bedfef6e2f7...12be1cca9a242dd97e15deed361a67d06788e92c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong style="font-weight: 600;">debian/changelog</strong></a>
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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="plaintext">python-pybedtools (0.10.0-3) unstable; urgency=medium</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="LC2" class="line" lang="plaintext"></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="LC3" class="line" lang="plaintext"> * Team Upload.</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">
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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="plaintext"> * d/patches/fix-doctest-imports.py: Add patch from upstream to use</span>
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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">
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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="plaintext"> explicit namespace in docstrings of long_range_interaction file (Closes:</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="LC6" class="line" lang="plaintext"> #1090283).</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="LC7" class="line" lang="plaintext"></span>
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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">
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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="plaintext"> -- Emmanuel Arias <eamanu@debian.org> Tue, 24 Dec 2024 19:24:47 -0300</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="LC9" class="line" lang="plaintext"></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="LC10" class="line" lang="plaintext">python-pybedtools (0.10.0-2) unstable; urgency=medium</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="LC11" class="line" lang="plaintext"></span>
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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">
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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"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/python-pybedtools/-/compare/a63b21265eb3609c14e213d8ef721bedfef6e2f7...12be1cca9a242dd97e15deed361a67d06788e92c#6a9e6eacc49e6dc8c1c2b571ef0cb0a1740d209a"><strong style="font-weight: 600;">debian/patches/fix-doctest-imports.py</strong></a>
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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="python"><span class="n" style="color: #333333;">From</span> <span class="n" style="color: #333333;">df144d1b335c82dcc02252a0274e150363b69165</span> <span class="n" style="color: #333333;">Mon</span> <span class="n" style="color: #333333;">Sep</span> <span class="mi" style="color: #009999;">17</span> <span class="mi" style="color: #009999;">00</span><span class="p">:</span><span class="mi" style="color: #009999;">00</span><span class="p">:</span><span class="mi" style="color: #009999;">00</span> <span class="mi" style="color: #009999;">2001</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="LC2" class="line" lang="python"><span class="n" style="color: #333333;">From</span><span class="p">:</span> <span class="n" style="color: #333333;">Ryan</span> <span class="n" style="color: #333333;">Dale</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333333;">ryan</span><span class="p">.</span><span class="n" style="color: #333333;">dale</span><span class="nd">@nih.gov</span><span class="o" style="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="LC4" class="line" lang="python"><span class="n" style="color: #333333;">Subject</span><span class="p">:</span> <span class="p">[</span><span class="n" style="color: #333333;">PATCH</span><span class="p">]</span> <span class="n" style="color: #333333;">use</span> <span class="n" style="color: #333333;">explicit</span> <span class="n" style="color: #333333;">namespace</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">docstrings</span> <span class="n" style="color: #333333;">of</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="LC5" class="line" lang="python"> <span class="n" style="color: #333333;">long_range_interaction</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="LC6" class="line" lang="python"></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="LC7" class="line" lang="python"><span class="o" style="font-weight: 600;">---</span></span>
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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">
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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="python"> <span class="n" style="color: #333333;">pybedtools</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">contrib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">long_range_interaction</span><span class="p">.</span><span class="n" style="color: #333333;">py</span> <span class="o" style="font-weight: 600;">|</span> <span class="mi" style="color: #009999;">8</span> <span class="o" style="font-weight: 600;">++++----</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="python"> <span class="mi" style="color: #009999;">1</span> <span class="nb" style="color: #0086b3;">file</span> <span class="n" style="color: #333333;">changed</span><span class="p">,</span> <span class="mi" style="color: #009999;">4</span> <span class="nf" style="color: #990000; font-weight: 600;">insertions</span><span class="p">(</span><span class="o" style="font-weight: 600;">+</span><span class="p">),</span> <span class="mi" style="color: #009999;">4</span> <span class="nf" style="color: #990000; font-weight: 600;">deletions</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="p">)</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="python"></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="python"><span class="n" style="color: #333333;">diff</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333333;">git</span> <span class="n" style="color: #333333;">a</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">pybedtools</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">contrib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">long_range_interaction</span><span class="p">.</span><span class="n" style="color: #333333;">py</span> <span class="n" style="color: #333333;">b</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">pybedtools</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">contrib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">long_range_interaction</span><span class="p">.</span><span class="n" style="color: #333333;">py</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="LC12" class="line" lang="python"><span class="n" style="color: #333333;">index</span> <span class="mi" style="color: #009999;">8</span><span class="n" style="color: #333333;">baffe74</span><span class="p">..</span><span class="n" style="color: #333333;">a3555a5c</span> <span class="mi" style="color: #009999;">100644</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="LC13" class="line" lang="python"><span class="o" style="font-weight: 600;">---</span> <span class="n" style="color: #333333;">a</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">pybedtools</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">contrib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">long_range_interaction</span><span class="p">.</span><span class="n" style="color: #333333;">py</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="python"><span class="o" style="font-weight: 600;">+++</span> <span class="n" style="color: #333333;">b</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">pybedtools</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">contrib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">long_range_interaction</span><span class="p">.</span><span class="n" style="color: #333333;">py</span></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">
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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="python"><span class="o" style="font-weight: 600;">@@</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">120</span><span class="p">,</span><span class="mi" style="color: #009999;">7</span> <span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">120</span><span class="p">,</span><span class="mi" style="color: #009999;">7</span> <span class="o" style="font-weight: 600;">@@</span> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">tag_bedpe</span><span class="p">(</span><span class="n" style="color: #333333;">bedpe</span><span class="p">,</span> <span class="n" style="color: #333333;">queries</span><span class="p">,</span> <span class="n" style="color: #333333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999999;">False</span><span class="p">):</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="python"> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">queries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">OrderedDict</span><span class="p">()</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="python"> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">queries</span><span class="p">[</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">tss</span><span class="sh" style="color: #dd1144;">'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">tsses</span></span>
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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="python"> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">queries</span><span class="p">[</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">pk</span><span class="sh" style="color: #dd1144;">'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">peaks</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="python"><span class="o" style="font-weight: 600;">-</span> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">iterator</span><span class="p">,</span> <span class="n" style="color: #333333;">n</span><span class="p">,</span> <span class="n" style="color: #333333;">extra</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">tag_bedpe</span><span class="p">(</span><span class="n" style="color: #333333;">bedpe</span><span class="p">,</span> <span class="n" style="color: #333333;">queries</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="20" 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">
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="python"><span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">iterator</span><span class="p">,</span> <span class="n" style="color: #333333;">n</span><span class="p">,</span> <span class="n" style="color: #333333;">extra</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">pybedtools</span><span class="p">.</span><span class="n" style="color: #333333;">contrib</span><span class="p">.</span><span class="n" style="color: #333333;">long_range_interaction</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">tag_bedpe</span><span class="p">(</span><span class="n" style="color: #333333;">bedpe</span><span class="p">,</span> <span class="n" style="color: #333333;">queries</span><span class="p">)</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="python"> <span class="o" style="font-weight: 600;">>>></span> <span class="nf" style="color: #990000; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333333;">n</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="22" 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">
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="python"> <span class="mi" style="color: #009999;">2</span></span>
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<td class="new_line diff-line-num new" data-linenumber="23" 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">
23
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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="LC23" class="line" lang="python"> <span class="o" style="font-weight: 600;">>>></span> <span class="nf" style="color: #990000; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333333;">extra</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="24" 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">
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="python"><span class="o" style="font-weight: 600;">@@</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">280</span><span class="p">,</span><span class="mi" style="color: #009999;">7</span> <span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">280</span><span class="p">,</span><span class="mi" style="color: #009999;">7</span> <span class="o" style="font-weight: 600;">@@</span> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">cis_trans_interactions</span><span class="p">(</span><span class="n" style="color: #333333;">iterator</span><span class="p">,</span> <span class="n" style="color: #333333;">n</span><span class="p">,</span> <span class="n" style="color: #333333;">extra</span><span class="p">,</span> <span class="n" style="color: #333333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999999;">True</span><span class="p">):</span></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="python"> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">queries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">OrderedDict</span><span class="p">()</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="python"> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">queries</span><span class="p">[</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">tss</span><span class="sh" style="color: #dd1144;">'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">tsses</span></span>
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<td class="new_line diff-line-num new" data-linenumber="27" 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">
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="python"> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">queries</span><span class="p">[</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">pk</span><span class="sh" style="color: #dd1144;">'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">peaks</span></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="python"><span class="o" style="font-weight: 600;">-</span> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">iterator</span><span class="p">,</span> <span class="n" style="color: #333333;">n</span><span class="p">,</span> <span class="n" style="color: #333333;">extra</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">tag_bedpe</span><span class="p">(</span><span class="n" style="color: #333333;">bedpe</span><span class="p">,</span> <span class="n" style="color: #333333;">queries</span><span class="p">)</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="python"><span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">iterator</span><span class="p">,</span> <span class="n" style="color: #333333;">n</span><span class="p">,</span> <span class="n" style="color: #333333;">extra</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">pybedtools</span><span class="p">.</span><span class="n" style="color: #333333;">contrib</span><span class="p">.</span><span class="n" style="color: #333333;">long_range_interaction</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">tag_bedpe</span><span class="p">(</span><span class="n" style="color: #333333;">bedpe</span><span class="p">,</span> <span class="n" style="color: #333333;">queries</span><span class="p">)</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="python"> <span class="o" style="font-weight: 600;">>>></span> <span class="nf" style="color: #990000; font-weight: 600;">for </span><span class="p">(</span><span class="n" style="color: #333333;">label</span><span class="p">,</span> <span class="n" style="color: #333333;">group1</span><span class="p">,</span> <span class="n" style="color: #333333;">group2</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">iterator</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="31" 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">
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="python"> <span class="p">...</span> <span class="n" style="color: #333333;">group1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">sorted</span><span class="p">(</span><span class="n" style="color: #333333;">group1</span><span class="p">,</span> <span class="n" style="color: #333333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333333;">x</span><span class="p">:</span> <span class="nf" style="color: #990000; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333333;">x</span><span class="p">))</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="python"> <span class="p">...</span> <span class="n" style="color: #333333;">group2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">sorted</span><span class="p">(</span><span class="n" style="color: #333333;">group2</span><span class="p">,</span> <span class="n" style="color: #333333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333333;">x</span><span class="p">:</span> <span class="nf" style="color: #990000; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333333;">x</span><span class="p">))</span></span>
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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="python"><span class="o" style="font-weight: 600;">@@</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">303</span><span class="p">,</span><span class="mi" style="color: #009999;">8</span> <span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">303</span><span class="p">,</span><span class="mi" style="color: #009999;">8</span> <span class="o" style="font-weight: 600;">@@</span> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">cis_trans_interactions</span><span class="p">(</span><span class="n" style="color: #333333;">iterator</span><span class="p">,</span> <span class="n" style="color: #333333;">n</span><span class="p">,</span> <span class="n" style="color: #333333;">extra</span><span class="p">,</span> <span class="n" style="color: #333333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999999;">True</span><span class="p">):</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="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">that</span> <span class="n" style="color: #333333;">they</span> <span class="n" style="color: #333333;">are</span> <span class="n" style="color: #333333;">also</span> <span class="n" style="color: #333333;">connected</span> <span class="n" style="color: #333333;">to</span> <span class="n" style="color: #333333;">gene3</span><span class="p">:</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="python"> </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="python"> <span class="o" style="font-weight: 600;">>>></span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">pandas</span><span class="p">;</span> <span class="n" style="color: #333333;">pandas</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">set_option</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">display.max_columns</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="mi" style="color: #009999;">10</span><span class="p">)</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="python"><span class="o" style="font-weight: 600;">-</span> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">iterator</span><span class="p">,</span> <span class="n" style="color: #333333;">n</span><span class="p">,</span> <span class="n" style="color: #333333;">extra</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">tag_bedpe</span><span class="p">(</span><span class="n" style="color: #333333;">bedpe</span><span class="p">,</span> <span class="p">{</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">tss</span><span class="sh" style="color: #dd1144;">'</span><span class="p">:</span> <span class="n" style="color: #333333;">tsses</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">pk</span><span class="sh" style="color: #dd1144;">'</span><span class="p">:</span> <span class="n" style="color: #333333;">peaks</span><span class="p">})</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="python"><span class="o" style="font-weight: 600;">-</span> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">cis_trans_interactions</span><span class="p">(</span><span class="n" style="color: #333333;">iterator</span><span class="p">,</span> <span class="n" style="color: #333333;">n</span><span class="p">,</span> <span class="n" style="color: #333333;">extra</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="39" 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">
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="python"><span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">iterator</span><span class="p">,</span> <span class="n" style="color: #333333;">n</span><span class="p">,</span> <span class="n" style="color: #333333;">extra</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">pybedtools</span><span class="p">.</span><span class="n" style="color: #333333;">contrib</span><span class="p">.</span><span class="n" style="color: #333333;">long_range_interaction</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">tag_bedpe</span><span class="p">(</span><span class="n" style="color: #333333;">bedpe</span><span class="p">,</span> <span class="p">{</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">tss</span><span class="sh" style="color: #dd1144;">'</span><span class="p">:</span> <span class="n" style="color: #333333;">tsses</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">pk</span><span class="sh" style="color: #dd1144;">'</span><span class="p">:</span> <span class="n" style="color: #333333;">peaks</span><span class="p">})</span></span>
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<td class="new_line diff-line-num new" data-linenumber="40" 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">
40
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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="LC40" class="line" lang="python"><span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">pybedtools</span><span class="p">.</span><span class="n" style="color: #333333;">contrib</span><span class="p">.</span><span class="n" style="color: #333333;">long_range_interaction</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">cis_trans_interactions</span><span class="p">(</span><span class="n" style="color: #333333;">iterator</span><span class="p">,</span> <span class="n" style="color: #333333;">n</span><span class="p">,</span> <span class="n" style="color: #333333;">extra</span><span class="p">)</span></span>
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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="python"> <span class="o" style="font-weight: 600;">>>></span> <span class="nf" style="color: #990000; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333333;">df</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">sort_values</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333333;">df</span><span class="p">.</span><span class="n" style="color: #333333;">columns</span><span class="p">)).</span><span class="nf" style="color: #990000; font-weight: 600;">reset_index</span><span class="p">(</span><span class="n" style="color: #333333;">drop</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999999;">True</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="42" 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">
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="python"> <span class="n" style="color: #333333;">target_label</span> <span class="n" style="color: #333333;">target_name</span> <span class="n" style="color: #333333;">cis_label</span> <span class="n" style="color: #333333;">cis_name</span> <span class="n" style="color: #333333;">distal_label</span> <span class="n" style="color: #333333;">distal_name</span> <span class="n" style="color: #333333;">label</span></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="python"> <span class="mi" style="color: #009999;">0</span> <span class="n" style="color: #333333;">pk</span> <span class="n" style="color: #333333;">peak1</span> <span class="n" style="color: #333333;">tss</span> <span class="n" style="color: #333333;">gene1</span> <span class="p">.</span> <span class="p">.</span> <span class="n" style="color: #333333;">pair2</span></span></pre></td>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/python-pybedtools/-/compare/a63b21265eb3609c14e213d8ef721bedfef6e2f7...12be1cca9a242dd97e15deed361a67d06788e92c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong style="font-weight: 600;">debian/patches/series</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -4,3 +4,4 @@ remove_badges_from_documentation.patch</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="LC4" class="line" lang="plaintext">add_missing_shebang.patch</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="LC5" class="line" lang="plaintext">yaml_safe_load.patch</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="LC6" class="line" lang="plaintext">416.patch</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="LC7" class="line" lang="plaintext">fix-doctest-imports.py</span></pre></td>
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