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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-bx">Debian Med / python-bx</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-bx/commit/e14ba32d8e332c3a490195aba1d5ff24f1efddc1">e14ba32d</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-07-23T13:08:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bye bye Python 2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-bx/commit/d00e2e62745b03285ebe9f67f89095b0a7769084">d00e2e62</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-07-23T13:09:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-bx/commit/6b86e1d861062565c5ca001d3055b70aee0a3a14">6b86e1d8</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-07-23T13:09:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.8.4'
Update to upstream version '0.8.4'
with Debian dir 92686d1069d5d6e3c39b848ba439cfcf7d686e33</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-bx/commit/8ba7414e6c63650488dd76a932e6e4b3f10bc006">8ba7414e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-07-23T13:48:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">0.8.4-1
</pre>
</li>
</ul>
<h4>23 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
debian/README.Debian
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<span class="new-file">
+
debian/lintian-overrides
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<li class="file-stats">
<a href="#f1d2114cd3a8dc8d0ef16427c845b6d73eb903da">
<span class="deleted-file">
−
debian/python-bx-tools.dirs
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<li class="file-stats">
<a href="#7ab752794ab93ad787b0758169191e19c77519ae">
<span class="deleted-file">
−
debian/python-bx-tools.lintian-overrides
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<li class="file-stats">
<a href="#4932e3db14a9df9f47677fe8fd7357d2a10d4f4b">
<span class="deleted-file">
−
debian/python-bx.dirs
</span>
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<li class="file-stats">
<a href="#1fbc5bffd5a0b967d201717f9b7a70c631945fdd">
<span class="deleted-file">
−
debian/python-bx.install
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<li class="file-stats">
<a href="#7e9c2e882eaa68e0997c620a5e832848331005fd">
<span class="deleted-file">
−
debian/python3-bx-tools.dirs
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<li class="file-stats">
<a href="#f449a50306e2f0ae20cbe1e9ae924e403186dcd3">
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−
debian/python3-bx-tools.lintian-overrides
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<a href="#5315cf9977ff6dcfcfb7d8d8d7db37dfe8b2bfc4">
<span class="deleted-file">
−
debian/python3-bx.dirs
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<li class="file-stats">
<a href="#58daef06ce1993be0d7607c90ceac9ded86eb6b4">
<span class="deleted-file">
−
debian/python3-bx.install
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#40ab2307cc3e5eb970b3a70221d81e7e45f4562f">
doc/source/index.rst
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<li class="file-stats">
<a href="#21206bf3275bd0d8047efb74ab72099debee67b8">
lib/bx/align/score_tests.py
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<li class="file-stats">
<a href="#0a89409d04b7f18042928eb97a444e22750e9409">
lib/bx/bbi/bpt_file.pyx
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<li class="file-stats">
<a href="#f9e5eea87ec841d5444be43728727460c0be590d">
lib/bx/bitset_tests.py
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<li class="file-stats">
<a href="#afc52934ef927f0b735fed3d6f32f32ede6ea92a">
lib/bx/seq/twobit.py
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<li class="file-stats">
<a href="#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">
setup.cfg
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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</ul>
<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,3 +22,6 @@ nose*.egg</td>
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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"># .eggs directory</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">.eggs</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"># Virtualenv</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.venv</span></pre>
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<br>
</li>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1
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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2
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<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;"><span class="idiff left">sudo</span></span><span class="pi"><span class="idiff">:</span></span><span class="idiff"> </span><span class="no" style="color: #008080;"><span class="idiff right">false</span></span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;"><span class="idiff left">cache</span></span><span class="pi"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">pip</span></span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">os</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">linux</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;">## - osx</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">linux</span></span>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">2.7</span></span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">3.3</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">2.7'</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.5'</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">global</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">PYTHON=python</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">TWINE_USERNAME=nsoranzo</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">secure</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">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'</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">_deploy_common</span><span class="pi">:</span> <span class="nl">&deploy_common</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">tag IS present</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$PYTHON -m pip install cibuildwheel twine</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">deploy</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.5'</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">services</span><span class="pi">:</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docker</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">CIBW_BEFORE_BUILD="yum install -y zlib-devel && pip install Cython numpy"</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*deploy_common</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cibuildwheel --output-dir dist</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$PYTHON -m pip install Cython nose numpy python-lzo six</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$PYTHON setup.py build_ext --inplace</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$PYTHON setup.py sdist</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">twine check dist/*</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">twine upload --skip-existing dist/*</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">deploy</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">generic</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">PYTHON=python3</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CIBW_BEFORE_BUILD="pip install Cython numpy"</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span> <span class="pi">{}</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*deploy_common</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cibuildwheel --output-dir dist</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">twine check dist/*</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">twine upload --skip-existing dist/*</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="yaml"><span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">liblzo2-dev</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Use miniconda for dependencies, pip is too slow -- https://gist.github.com/zonca/9958333</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">chmod +x miniconda.sh</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./miniconda.sh -b</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH=/home/travis/miniconda2/bin:$PATH</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda update --yes conda</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span> </span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda create --yes -n testenv python=$TRAVIS_PYTHON_VERSION Cython numpy nose</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">source activate testenv</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install python-lzo</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py build_ext --inplace</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py install</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> </span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">nosetests</span></span></pre>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">liblzo2-dev</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$PYTHON -m pip install Cython nose numpy python-lzo six</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$PYTHON setup.py build_ext --inplace</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$PYTHON setup.py install</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">nosetests</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are:</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p"> *</span> Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"><span class="p"> *</span> Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; opt<span class="idiff left right">o</span>mized for use over network filesystems)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p"> *</span> Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; opt<span class="idiff left right">i</span>mized for use over network filesystems)</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="p"> *</span> Data structures for working with intervals on sequences</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="p"> *</span> "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p"> *</span> "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation</span>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">python-bx for Debian</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">--------------------</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">The situation is somewhat unfortunate in that both python2 and python3</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">occupy the same location in /usr/bin. The -tools packages separate those</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">binaries from the modules.</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">The language suffix ".py" was left for the time being for compatibility</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">with the installation of the same on other distributions and wary of</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">reverse dependencies.</span>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-bx (0.8.4-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream release. Removed Python2 binary packages; enabled the tests</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Tue, 23 Jul 2019 15:10:11 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">python-bx (0.8.2-1) unstable; urgency=low</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream version.</span>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,55 +8,26 @@ Build-Depends:</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> debhelper (>= 9),</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># Python2</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> python-setuptools,</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> python-all-dev,</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> python-nose,</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> python-numpy,</span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> cython,</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"># Python3</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3-setuptools,</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-all-dev,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python3-lzo,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> python3-nose,</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> python3-numpy,</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> python3-six,</span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> cython3</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Standards-Version: 4.2.1</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: https://github.com/bxlab/bx-python</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-bx.git</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-bx</span>
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27
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">Package: python-bx</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">Depends:</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">Description: library to manage genomic data and its aligment</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> The bx-python project is a python library and associated set of scripts to</span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> allow for rapid implementation of genome scale analyses. The library contains</span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> a variety of useful modules, but the particular strengths are:</span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> * Classes for reading and working with genome-scale multiple local</span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> alignments (in MAF, AXT, and LAV formats)</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> * Generic data structure for indexing on disk files that contain blocks of</span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> data associated with intervals on various sequences (used, for example, to</span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> provide random access to individual alignments in huge files; optimized for</span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> use over network filesystems)</span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> * Data structures for working with intervals on sequences</span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> * "Binned bitsets" which act just like chromosome sized bit arrays, but</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> lazily allocate regions and allow large blocks of all set or all unset bits</span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> to be stored compactly</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> * "Intersecter" for performing fast intersection tests that preserve both</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> query and target intervals and associated annotation</span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> This package provides the Python 2 library.</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Package: python3-bx</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">Depends:</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">Recommends: python-bx-tools</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Depends: python3-lzo,</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Replaces: python3-bx-tools</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Provides: python3-bx-tools</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Description: library to manage genomic data and its alignment</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> The bx-python project is a python library and associated set of scripts to</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> allow for rapid implementation of genome scale analyses. The library contains</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,21 +44,3 @@ Description: library to manage genomic data and its alignment</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> to be stored compactly</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> * "Intersecter" for performing fast intersection tests that preserve both</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> query and target intervals and associated annotation</span></pre>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"> This package provides the Python 3 library.</span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">Package: python-bx-tools</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">Conflicts: python3-bx-tools</span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">Depends: python-bx, ${misc:Depends}, ${python:Depends}</span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">Description: command line interface to python3-bx</span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext"> This package collects all command line tools to access the functionality</span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"> of the python-bx library. All scripts have python2 in their shebang line.</span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext"></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext">Package: python3-bx-tools</span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">Architecture: all</span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">Conflicts: python-bx-tools</span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">Depends: python3-bx, ${misc:Depends}, ${python3:Depends}</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">Description: command line interface to python3-bx</span>
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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"> This package collects all command line tools to access the functionality</span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext"> of the python-bx library. All scripts have python3 in their shebang line.</span></pre>
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<li id="efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># Not fiddling with .py endings because of reverse-dependencies expected from toil</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># We shall revisit this decision once all packages for toil are in the distribution</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># and we have learned more about how bx is used in the community in 3rd party scripts.</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/aggregate_scores_in_intervals.py</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/align_print_template.py</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/axt_extract_ranges.py</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/axt_to_fasta.py</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/axt_to_lav.py</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/axt_to_maf.py</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_bigwig_profile.py</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_build_windows.py</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_complement.py</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_count_by_interval.py</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_count_overlapping.py</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_coverage.py</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_coverage_by_interval.py</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_diff_basewise_summary.py</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_extend_to.py</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_intersect.py</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_intersect_basewise.py</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_merge_overlapping.py</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_rand_intersect.py</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bed_subtract_basewise.py</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/bnMapper.py</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/div_snp_table_chr.py</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/find_in_sorted_file.py</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/gene_fourfold_sites.py</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/get_scores_in_intervals.py</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/int_seqs_to_char_strings.py</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/interval_count_intersections.py</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/interval_join.py</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/lav_to_axt.py</span>
</pre>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/lav_to_maf.py</span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/line_select.py</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/lzop_build_offset_table.py</span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/mMK_bitset.py</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_build_index.py</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_chop.py</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_chunk.py</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_col_counts.py</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_col_counts_all.py</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_count.py</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_covered_ranges.py</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_covered_regions.py</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_div_sites.py</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_drop_overlapping.py</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_extract_chrom_ranges.py</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_extract_ranges.py</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_extract_ranges_indexed.py</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_filter.py</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_filter_max_wc.py</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_gap_frequency.py</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_gc_content.py</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_interval_alignibility.py</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_limit_to_species.py</span>
</pre>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_mapping_word_frequency.py</span>
</pre>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_mask_cpg.py</span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_mean_length_ungapped_piece.py</span>
</pre>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_percent_columns_matching.py</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_percent_identity.py</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_print_chroms.py</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_print_scores.py</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_randomize.py</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_region_coverage_by_src.py</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_select.py</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_shuffle_columns.py</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_species_in_all_files.py</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_split_by_src.py</span>
</pre>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_thread_for_species.py</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_tile.py</span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_tile_2.py</span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_tile_2bit.py</span>
</pre>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_to_axt.py</span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_to_concat_fasta.py</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_to_fasta.py</span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_to_int_seqs.py</span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_translate_chars.py</span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_truncate.py</span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/maf_word_frequency.py</span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/mask_quality.py</span>
</pre>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/nib_chrom_intervals_to_fasta.py</span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/nib_intervals_to_fasta.py</span>
</pre>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/nib_length.py</span>
</pre>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/one_field_per_line.py</span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/out_to_chain.py</span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/prefix_lines.py</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/pretty_table.py</span>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/qv_to_bqv.py</span>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/random_lines.py</span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/table_add_column.py</span>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/table_filter.py</span>
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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/tfloc_summary.py</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/ucsc_gene_table_to_intervals.py</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/wiggle_to_array_tree.py</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/wiggle_to_binned_array.py</span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/wiggle_to_chr_binned_array.py</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">python3-bx: script-with-language-extension usr/bin/wiggle_to_simple.py</span></pre>
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<li id="f1d2114cd3a8dc8d0ef16427c845b6d73eb903da">
<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#f1d2114cd3a8dc8d0ef16427c845b6d73eb903da"><strong>debian/python-bx-tools.dirs</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr</span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#7ab752794ab93ad787b0758169191e19c77519ae"><strong>debian/python-bx-tools.lintian-overrides</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># Not fiddling with .py endings because of reverse-dependencies expected from toil</span>
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2
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"># We shall revisit this decision once all packages for toil are in the distribution</span>
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3
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"># and we have learned more about how bx is used in the community in 3rd party scripts.</span>
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4
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/aggregate_scores_in_intervals.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/align_print_template.py</span>
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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/axt_extract_ranges.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/axt_to_fasta.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/axt_to_lav.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/axt_to_maf.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_bigwig_profile.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_build_windows.py</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_complement.py</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_count_by_interval.py</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_count_overlapping.py</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_coverage.py</span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_coverage_by_interval.py</span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_diff_basewise_summary.py</span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_extend_to.py</span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_intersect.py</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_intersect_basewise.py</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_merge_overlapping.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_rand_intersect.py</span>
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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bed_subtract_basewise.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/bnMapper.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/div_snp_table_chr.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/find_in_sorted_file.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/gene_fourfold_sites.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/get_scores_in_intervals.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
29
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/int_seqs_to_char_strings.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/interval_count_intersections.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/interval_join.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
32
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/lav_to_axt.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
33
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/lav_to_maf.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
34
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/line_select.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
35
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/lzop_build_offset_table.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/mMK_bitset.py</span>
</pre>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_build_index.py</span>
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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
38
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_chop.py</span>
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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
39
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_chunk.py</span>
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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_col_counts.py</span>
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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
41
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_col_counts_all.py</span>
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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
42
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_count.py</span>
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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
43
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_covered_ranges.py</span>
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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
44
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_covered_regions.py</span>
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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
45
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_div_sites.py</span>
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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
46
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_drop_overlapping.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
47
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_extract_chrom_ranges.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_extract_ranges.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_extract_ranges_indexed.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
50
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_filter.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
51
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_filter_max_wc.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
52
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_gap_frequency.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
53
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_gc_content.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
54
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_interval_alignibility.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
55
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_limit_to_species.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
56
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_mapping_word_frequency.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
57
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_mask_cpg.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
58
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_mean_length_ungapped_piece.py</span>
</pre>
</td>
</tr>
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<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
59
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_percent_columns_matching.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
60
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_percent_identity.py</span>
</pre>
</td>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_print_chroms.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
62
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_print_scores.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
63
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_randomize.py</span>
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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
64
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_region_coverage_by_src.py</span>
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<td class="diff-line-num old old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
65
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_select.py</span>
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<td class="diff-line-num old old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
66
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_shuffle_columns.py</span>
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<td class="diff-line-num old old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
67
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_species_in_all_files.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
68
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_split_by_src.py</span>
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<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
69
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_thread_for_species.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
70
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_tile.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
71
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_tile_2.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
72
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_tile_2bit.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
73
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_to_axt.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
74
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_to_concat_fasta.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
75
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_to_fasta.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
76
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_to_int_seqs.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
77
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_translate_chars.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
78
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_truncate.py</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
79
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/maf_word_frequency.py</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
80
</td>
<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/mask_quality.py</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
81
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/nib_chrom_intervals_to_fasta.py</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
82
</td>
<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/nib_intervals_to_fasta.py</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
83
</td>
<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/nib_length.py</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
84
</td>
<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/one_field_per_line.py</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
85
</td>
<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/out_to_chain.py</span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/prefix_lines.py</span>
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<td class="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/pretty_table.py</span>
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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/qv_to_bqv.py</span>
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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/random_lines.py</span>
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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/table_add_column.py</span>
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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/table_filter.py</span>
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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/tfloc_summary.py</span>
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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/ucsc_gene_table_to_intervals.py</span>
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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/wiggle_to_array_tree.py</span>
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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/wiggle_to_binned_array.py</span>
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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/wiggle_to_chr_binned_array.py</span>
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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext">python-bx-tools: script-with-language-extension usr/bin/wiggle_to_simple.py</span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#4932e3db14a9df9f47677fe8fd7357d2a10d4f4b"><strong>debian/python-bx.dirs</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/bin</span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#1fbc5bffd5a0b967d201717f9b7a70c631945fdd"><strong>debian/python-bx.install</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="c1" style="color: #998; font-style: italic;">#usr/bin</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#7e9c2e882eaa68e0997c620a5e832848331005fd"><strong>debian/python3-bx-tools.dirs</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr</span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#f449a50306e2f0ae20cbe1e9ae924e403186dcd3"><strong>debian/python3-bx-tools.lintian-overrides</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># Not fiddling with .py endings because of reverse-dependencies expected from toil</span>
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2
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"># We shall revisit this decision once all packages for toil are in the distribution</span>
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3
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"># and we have learned more about how bx is used in the community in 3rd party scripts.</span>
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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/aggregate_scores_in_intervals.py</span>
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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/align_print_template.py</span>
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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/axt_extract_ranges.py</span>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/axt_to_fasta.py</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/axt_to_lav.py</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/axt_to_maf.py</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_bigwig_profile.py</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_build_windows.py</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_complement.py</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_count_by_interval.py</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_count_overlapping.py</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_coverage.py</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_coverage_by_interval.py</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_diff_basewise_summary.py</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_extend_to.py</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_intersect.py</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_intersect_basewise.py</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_merge_overlapping.py</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_rand_intersect.py</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bed_subtract_basewise.py</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/bnMapper.py</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/div_snp_table_chr.py</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/find_in_sorted_file.py</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/gene_fourfold_sites.py</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/get_scores_in_intervals.py</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/int_seqs_to_char_strings.py</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/interval_count_intersections.py</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/interval_join.py</span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/lav_to_axt.py</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/lav_to_maf.py</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/line_select.py</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/lzop_build_offset_table.py</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/mMK_bitset.py</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_build_index.py</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_chop.py</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_chunk.py</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_col_counts.py</span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_col_counts_all.py</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_count.py</span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_covered_ranges.py</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_covered_regions.py</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_div_sites.py</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_drop_overlapping.py</span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_extract_chrom_ranges.py</span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_extract_ranges.py</span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_extract_ranges_indexed.py</span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_filter.py</span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_filter_max_wc.py</span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_gap_frequency.py</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_gc_content.py</span>
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<td class="diff-line-num old old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_interval_alignibility.py</span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_limit_to_species.py</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_mapping_word_frequency.py</span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_mask_cpg.py</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_mean_length_ungapped_piece.py</span>
</pre>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_percent_columns_matching.py</span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_percent_identity.py</span>
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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_print_chroms.py</span>
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<td class="diff-line-num old old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
62
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_print_scores.py</span>
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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
63
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_randomize.py</span>
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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
64
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_region_coverage_by_src.py</span>
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<td class="diff-line-num old old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
65
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_select.py</span>
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<td class="diff-line-num old old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
66
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_shuffle_columns.py</span>
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<td class="diff-line-num old old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
67
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_species_in_all_files.py</span>
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<td class="diff-line-num old old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
68
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_split_by_src.py</span>
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<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_thread_for_species.py</span>
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<td class="diff-line-num old old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_tile.py</span>
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<td class="diff-line-num old old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_tile_2.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
72
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_tile_2bit.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_to_axt.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
74
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_to_concat_fasta.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
75
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_to_fasta.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
76
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_to_int_seqs.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
77
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_translate_chars.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
78
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_truncate.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
79
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/maf_word_frequency.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
80
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/mask_quality.py</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
81
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/nib_chrom_intervals_to_fasta.py</span>
</pre>
</td>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/nib_intervals_to_fasta.py</span>
</pre>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/nib_length.py</span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/one_field_per_line.py</span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/out_to_chain.py</span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/prefix_lines.py</span>
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<td class="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/pretty_table.py</span>
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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/qv_to_bqv.py</span>
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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/random_lines.py</span>
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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/table_add_column.py</span>
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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/table_filter.py</span>
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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/tfloc_summary.py</span>
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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/ucsc_gene_table_to_intervals.py</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/wiggle_to_array_tree.py</span>
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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/wiggle_to_binned_array.py</span>
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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/wiggle_to_chr_binned_array.py</span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext">python3-bx-tools: script-with-language-extension usr/bin/wiggle_to_simple.py</span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#5315cf9977ff6dcfcfb7d8d8d7db37dfe8b2bfc4"><strong>debian/python3-bx.dirs</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/bin</span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#58daef06ce1993be0d7607c90ceac9ded86eb6b4"><strong>debian/python3-bx.install</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="c1" style="color: #998; font-style: italic;">#usr/bin</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,15 +6,11 @@</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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7
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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8
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">export NOSE_VERBOSE=2</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">export PYBUILD_DESTDIR_python2=debian/python-bx/</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">#export PYBUILD_DESTDIR_python2-dbg=debian/python-foo-dbg/</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">export PYBUILD_DESTDIR_python3=debian/python3-bx/</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">#export PYBUILD_DESTDIR_python3-dbg=debian/python3-foo-dbg/</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">export PYBUILD_NAME=bx-python</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST=cp -r {dir}/test_data {build_dir}/</span>
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15
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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16
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">%:</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">2,python</span>3 --buildsystem=pybuild</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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18
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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19
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">override_dh_auto_clean:</span>
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20
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> dh_auto_clean</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,13 +20,9 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># Changes perpetually redone</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> rm -rf lib/bx_python.egg-info</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> dh_install --autodest</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> mkdir -p $(CURDIR)/debian/python-bx-tools/usr</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> mv $(CURDIR)/debian/python-bx/usr/bin $(CURDIR)/debian/python-bx-tools/usr/</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> mkdir -p $(CURDIR)/debian/python3-bx-tools/usr</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> mv $(CURDIR)/debian/python3-bx/usr/bin $(CURDIR)/debian/python3-bx-tools/usr/</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"># override_dh_install:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"># dh_install --autodest</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"># dh_install</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"># mkdir -p $(CURDIR)/debian/python3-bx-tools/usr</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"># mv $(CURDIR)/debian/python3-bx/usr/bin $(CURDIR)/debian/python3-bx-tools/usr/</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span></pre>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> # skipped</span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#40ab2307cc3e5eb970b3a70221d81e7e45f4562f"><strong>doc/source/index.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ About bx-python</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are:</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats)</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> * Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; opt<span class="idiff left right">o</span>mized for use over network filesystems)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; opt<span class="idiff left right">i</span>mized for use over network filesystems)</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * Data structures for working with intervals on sequences</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation </span>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#21206bf3275bd0d8047efb74ab72099debee67b8"><strong>lib/bx/align/score_tests.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">Tests for `bx.align.score`.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">numpy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">array</span><span class="p">,</span> <span class="n" style="color: #333;">cumsum</span><span class="p">,</span> <span class="n" style="color: #333;">allclose</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,22 +9,21 @@ from six import StringIO</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">bx.align.maf</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">bx.align.score</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">aligns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="p">(</span> <span class="s" style="color: #d14;">"CCACTAGTTTTTAAATAATCTACTATCAAATAAAAGATTTGTTAATAATAAATTTTAAATCATTAACACTT"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="s" style="color: #d14;">"CCATTTGGGTTCAAAAATTGATCTATCA----------TGGTGGATTATTATTTAGCCATTAAGGACAAAT"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">111</span> <span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="p">(</span> <span class="s" style="color: #d14;">"CCACTAGTTTTTAAATAATCTAC-----AATAAAAGATTTGTTAATAAT---AAATTTTAAATCATTAA-----CACTT"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">"CCATTTGGGTTCAAAAATTGATCTATCA----------TGGTGGAT---TATTATTT-----AGCCATTAAGGACAAAT"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3626</span> <span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="p">(</span> <span class="s" style="color: #d14;">"CCACTAGTTTTTGATTC"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"CCATTTGGGTTC-----"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">299</span> <span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="p">(</span> <span class="s" style="color: #d14;">"CTTAGTTTTTGATCACC"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">"-----CTTGGGTTTACC"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">299</span> <span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="p">(</span> <span class="s" style="color: #d14;">"gggaattgaacaatgagaacacatggacacaggaaggggaacatcacacacc----------ggggcctgttgtggggtggggggaag"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">"ggaactagaacaagggagacacatacaaacaacaacaacaacaacacagcccttcccttcaaagagcttatagtctgatggaggagag"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="mi" style="color: #099;">1690</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">aligns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">"CCACTAGTTTTTAAATAATCTACTATCAAATAAAAGATTTGTTAATAATAAATTTTAAATCATTAACACTT"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">"CCATTTGGGTTCAAAAATTGATCTATCA----------TGGTGGATTATTATTTAGCCATTAAGGACAAAT"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">111</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"CCACTAGTTTTTAAATAATCTAC-----AATAAAAGATTTGTTAATAAT---AAATTTTAAATCATTAA-----CACTT"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="s" style="color: #d14;">"CCATTTGGGTTCAAAAATTGATCTATCA----------TGGTGGAT---TATTATTT-----AGCCATTAAGGACAAAT"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3626</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"CCACTAGTTTTTGATTC"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"CCATTTGGGTTC-----"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">299</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"CTTAGTTTTTGATCACC"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">"-----CTTGGGTTTACC"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">299</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"gggaattgaacaatgagaacacatggacacaggaaggggaacatcacacacc----------ggggcctgttgtggggtggggggaag"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">"ggaactagaacaagggagacacatacaaacaacaacaacaacaacacagcccttcccttcaaagagcttatagtctgatggaggagag"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="mi" style="color: #099;">1690</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">mafs</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""##maf</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;">a score=2883.0</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,54 +36,51 @@ s panTro1.chr1 49673 40 + 229575298 TGCGTGATTAATGCCTGAGATTGTGTGAAGTAAAA</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;">s rheMac1.SCAFFOLD45837 26063 33 - 31516 TGTGTGATTAATGCCTGAGATTGTGTGAAGTAA-------</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="n" style="color: #333;">nonsymm_scheme</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">build_scoring_scheme</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">""" A C G T</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="n" style="color: #333;">nonsymm_scheme</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">build_scoring_scheme</span><span class="p"><span class="idiff left right">(</span></span><span class="s" style="color: #d14;">""" A C G T</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;"> 91 0 -31 -123</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> -114 100 -125 -31</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> -31 -125 100 -114</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;"> -123 -31 -114 91 """</span><span class="p">,</span> <span class="mi" style="color: #099;">400</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;"> -123 -31 -114 91 """</span><span class="p">,</span> <span class="mi" style="color: #099;">400</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">aligns_for_nonsymm_scheme</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="p">(</span> <span class="s" style="color: #d14;">"AAAACCCCGGGGTTTT"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"ACGTACGTACGTACGT"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">580</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="n" style="color: #333;">aligns_for_nonsymm_scheme</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">"AAAACCCCGGGGTTTT"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"ACGTACGTACGTACGT"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">580</span><span class="p">)]</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"><span class="n" style="color: #333;">asymm_scheme</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">build_scoring_scheme</span> <span class="p">(</span> <span class="s" style="color: #d14;">""" 01 02 A C G T</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="n" style="color: #333;">asymm_scheme</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">build_scoring_scheme</span><span class="p">(</span><span class="s" style="color: #d14;">""" 01 02 A C G T</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;"> 01 200 -200 -50 100 -50 100</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> 02 -200 200 100 -50 100 -50 """</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gap1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="se" style="color: #d14;"><span class="idiff">\x00</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gap1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="se" style="color: #d14;"><span class="idiff">\x00</span></span><span class="s" style="color: #d14;"><span class="idiff right">'</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"><span class="n" style="color: #333;">aligns_for_asymm_scheme</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="p">(</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\x01\x01\x01\x01\x01\x01</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="s" style="color: #d14;">"ACGT</span><span class="se" style="color: #d14;">\x01\x02</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="mi" style="color: #099;">100</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"><span class="n" style="color: #333;">aligns_for_asymm_scheme</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\x01\x01\x01\x01\x01\x01</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="s" style="color: #d14;">"ACGT</span><span class="se" style="color: #d14;">\x01\x02</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="mi" style="color: #099;">100</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BasicTests</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">unittest</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">TestCase</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BasicTests</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">unittest</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">TestCase</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_scoring_text</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_scoring_text</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hox70</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t1</span><span class="p">,</span> <span class="n" style="color: #333;">t2</span><span class="p">,</span> <span class="n" style="color: #333;">score</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">aligns</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bx</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score_texts</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t2</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_align</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bx</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score_texts</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t2</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">score</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_align</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hox70</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">block</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Reader</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">StringIO</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mafs</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bx</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score_alignment</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">block</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">block</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_accumulate</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">block</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Reader</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">StringIO</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mafs</span></span><span class="p"><span class="idiff right">)</span>):</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bx</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score_alignment</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">block</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">block</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_accumulate</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hox70</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">allclose</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bx</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">accumulate_scores</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"-----CTTT"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"CTTAGTTTA"</span></span><span class="idiff right"> </span><span class="p">),</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">cumsum</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">430</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">30</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">30</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">30</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">30</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">31</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">91</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">91</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">123</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">allclose</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bx</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">accumulate_scores</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"-----CTTT"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"CTTAGTTTA"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">skip_ref_gaps</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">True</span></span><span class="idiff right"> </span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">cumsum</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">581</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">91</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">91</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">123</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">allclose</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">bx</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">accumulate_scores</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"-----CTTT"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"CTTAGTTTA"</span></span><span class="p">),</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">cumsum</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">([</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">430</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">30</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">30</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">30</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">30</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">31</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">91</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">91</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">123</span></span><span class="p"><span class="idiff right">])))</span>)</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">allclose</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">bx</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">accumulate_scores</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"-----CTTT"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"CTTAGTTTA"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">skip_ref_gaps</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">),</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">cumsum</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">([</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">581</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">91</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">91</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">123</span></span><span class="p"><span class="idiff right">])))</span>)</span></span>
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82
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_nonsymm_scoring</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_nonsymm_scoring</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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84
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nonsymm_scheme</span></span>
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85
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t1</span><span class="p">,</span> <span class="n" style="color: #333;">t2</span><span class="p">,</span> <span class="n" style="color: #333;">score</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">aligns_for_nonsymm_scheme</span><span class="p">:</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bx</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score_texts</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t2</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bx</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score_texts</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t2</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">score</span></span><span class="p">)</span></span>
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87
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_asymm_scoring</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_asymm_scoring</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">asymm_scheme</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t1</span><span class="p">,</span> <span class="n" style="color: #333;">t2</span><span class="p">,</span> <span class="n" style="color: #333;">score</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">aligns_for_asymm_scheme</span><span class="p">:</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bx</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score_texts</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t2</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="idiff right"> </span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bx</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score_texts</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t2</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">score</span></span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#0a89409d04b7f18042928eb97a444e22750e9409"><strong>lib/bx/bbi/bpt_file.pyx</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,7 +54,7 @@ cdef class BPTFile:</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> self.reader.read( self.key_size )</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> offset = self.reader.read_uint64()</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> # Loop until correct subtree is found</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> for i from 0 <= i < child_count:</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> for i from 0 <= i < child_count<span class="idiff left right"> - 1</span>:</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> node_key = self.reader.read( self.key_size )</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> if node_key > key:</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> break</span>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#f9e5eea87ec841d5444be43728727460c0be590d"><strong>lib/bx/bitset_tests.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,108 +5,115 @@ Tests for `bx.bitset`.</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">bx.bitset</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">AbstractTests</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">object</span> <span class="p">):</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">assert_bits</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">bits</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">list</span> <span class="p">),</span> <span class="s" style="color: #d14;">"Bitset size and verification list size do not match"</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEquals</span><span class="p">(</span> <span class="n" style="color: #333;">bits</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_overflow_create</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">,</span> <span class="mi" style="color: #099;">4000000000</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_overflow_access</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span> <span class="mi" style="color: #099;">100</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">IndexError</span><span class="p">,</span> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">IndexError</span><span class="p">,</span> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">,</span> <span class="mi" style="color: #099;">110</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_access</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">AbstractTests</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">assert_bits</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">bits</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">),</span> <span class="s" style="color: #d14;">"Bitset size and verification list size do not match"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span><span class="p">):</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">bits</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_overflow_create</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">,</span> <span class="mi" style="color: #099;">4000000000</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_overflow_access</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">IndexError</span><span class="p">,</span> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">IndexError</span><span class="p">,</span> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">,</span> <span class="mi" style="color: #099;">110</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_access</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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24
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create and assert empty</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff right"> </span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">l</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">100</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">bits</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">l</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Set some positions</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">11</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">14</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">70</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">16</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="idiff right"> </span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left">11</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">14</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">70</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">16</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">pos</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">pos</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Clear some positions</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">14</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">80</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">16</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clear</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="idiff right"> </span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">l</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left">14</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">80</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">16</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clear</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">pos</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">pos</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">bits</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">l</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_range_access</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_range_access</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create and assert empty</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff right"> </span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">l</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">100</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">bits</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">l</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Set some positions</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span> <span class="p">(</span> <span class="mi" style="color: #099;">11</span><span class="p">,</span> <span class="mi" style="color: #099;">14</span> <span class="p">),</span> <span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">75</span><span class="p">),</span> <span class="p">(</span><span class="mi" style="color: #099;">90</span><span class="p">,</span><span class="mi" style="color: #099;">99</span><span class="p">)</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span> <span class="p">):</span> <span class="n" style="color: #333;">l</span><span class="p">[</span> <span class="n" style="color: #333;">pos</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span> <span class="n" style="color: #333;">bits</span><span class="p">,</span> <span class="n" style="color: #333;">l</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">((</span><span class="mi" style="color: #099;">11</span><span class="p">,</span> <span class="mi" style="color: #099;">14</span><span class="p">),</span> <span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">75</span><span class="p">),</span> <span class="p">(</span><span class="mi" style="color: #099;">90</span><span class="p">,</span> <span class="mi" style="color: #099;">99</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span><span class="n" style="color: #333;">bits</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_count</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_count</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create and assert empty</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">100</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Set some positions</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">11</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">14</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">20</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">75</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">90</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span><span class="idiff left right"> </span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">count_range</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">count_range</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">20</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">count_range</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">25</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">25</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">25</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">count_range</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">80</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">20</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">10</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">count_range</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">68</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_find</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(<span class="idiff left">(</span></span><span class="mi" style="color: #099;"><span class="idiff">11</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">14</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">20</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">75</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">90</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff right">)</span>):</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">count_range</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">count_range</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">20</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">count_range</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">25</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">25</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">25</span></span><span class="p">)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">count_range</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">80</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">20</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">10</span></span><span class="p">)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">count_range</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">68</span></span><span class="p">)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_find</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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62
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create and assert empty</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">100</span></span><span class="p">)</span></span>
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64
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Set some positions</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">11</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">14</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">20</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">75</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">90</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span><span class="idiff left right"> </span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(<span class="idiff left">(</span></span><span class="mi" style="color: #099;"><span class="idiff">11</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">14</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">20</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">75</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">90</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff right">)</span>):</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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67
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Next set</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_set</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">11</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_set</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">13</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">13</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_set</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">15</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">20</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_set</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">11</span></span><span class="p">)</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_set</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">13</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">13</span></span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_set</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">15</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">20</span></span><span class="p">)</span></span>
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71
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Next clear</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_clear</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_clear</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">11</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">14</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_clear</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">20</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">75</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_clear</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">92</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_and</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">bits1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">bits2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">bits1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">20</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">40</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">bits2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">50</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">25</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">bits1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iand</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">bits2</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_clear</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_clear</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">11</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">14</span></span><span class="p">)</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_clear</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">20</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">75</span></span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">bits</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">next_clear</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">92</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">100</span></span><span class="p">)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_and</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">bits1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">100</span></span><span class="p">)</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">bits2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">100</span></span><span class="p">)</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">bits1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left">20</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">40</span></span><span class="p">)</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">bits2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left">50</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">25</span></span><span class="p">)</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">bits1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iand</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">bits2</span></span><span class="p">)</span></span>
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83
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">60</span> <span class="p">):</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span> <span class="n" style="color: #333;">bits1</span><span class="p">,</span> <span class="n" style="color: #333;">l</span> <span class="p">)</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> </span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_or</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">bits1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span> <span class="mi" style="color: #099;">100</span> <span class="p">)</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">bits2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span> <span class="mi" style="color: #099;">100</span> <span class="p">)</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">bits1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span> <span class="p">)</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">bits2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">25</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">bits1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ior</span><span class="p">(</span> <span class="n" style="color: #333;">bits2</span> <span class="p">)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">60</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span><span class="n" style="color: #333;">bits1</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_or</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">bits1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">bits2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">bits1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">bits2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span><span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">25</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">bits1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ior</span><span class="p">(</span><span class="n" style="color: #333;">bits2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">75</span> <span class="p">):</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span> <span class="n" style="color: #333;">bits1</span><span class="p">,</span> <span class="n" style="color: #333;">l</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> </span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_not</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span> <span class="mi" style="color: #099;">100</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span> <span class="p">)</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">75</span><span class="p">):</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span><span class="n" style="color: #333;">bits1</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_not</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_bits</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_range</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">invert</span><span class="p">()</span></span>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">60</span> <span class="p">):</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span> <span class="n" style="color: #333;">bits</span><span class="p">,</span> <span class="n" style="color: #333;">l</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BitSetTests</span><span class="p">(</span> <span class="n" style="color: #333;">AbstractTests</span><span class="p">,</span> <span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">new_bits</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">size</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bitset</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BitSet</span><span class="p">(</span> <span class="n" style="color: #333;">size</span> <span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BinnedBitSetTests</span><span class="p">(</span> <span class="n" style="color: #333;">AbstractTests</span><span class="p">,</span> <span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">new_bits</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">size</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">granularity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">11</span> </span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bitset</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BinnedBitSet</span><span class="p">(</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">granularity</span> <span class="p">)</span> </span></pre>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">60</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_bits</span><span class="p">(</span><span class="n" style="color: #333;">bits</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BitSetTests</span><span class="p">(</span><span class="n" style="color: #333;">AbstractTests</span><span class="p">,</span> <span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">new_bits</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">):</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bitset</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BitSet</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">)</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BinnedBitSetTests</span><span class="p">(</span><span class="n" style="color: #333;">AbstractTests</span><span class="p">,</span> <span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">new_bits</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">):</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">granularity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">11</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bitset</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BinnedBitSet</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">granularity</span><span class="p">)</span></span></pre>
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<li id="afc52934ef927f0b735fed3d6f32f32ede6ea92a">
<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#afc52934ef927f0b735fed3d6f32f32ede6ea92a"><strong>lib/bx/seq/twobit.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">Access to files containing sequence data in 'twobit' format.</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">struct</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">struct</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">calcsize</span><span class="p">,</span> <span class="n" style="color: #333;">unpack</span></span>
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7
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Mapping</span></span>
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8
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_twobit</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,8 +12,9 @@ TWOBIT_MAGIC_SIZE = 4</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">TWOBIT_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TwoBitSequence</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">object</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tbf</span><span class="p">,</span> <span class="n" style="color: #333;">header_offset</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TwoBitSequence</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tbf</span><span class="p">,</span> <span class="n" style="color: #333;">header_offset</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tbf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tbf</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">header_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header_offset</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,18 +22,18 @@ class TwoBitSequence( object ):</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_blocks</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">masked_blocks</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loaded</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__getitem__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">slice</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">stride</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">slice</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">indices</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__getitem__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">slice</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">stride</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">slice</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">indices</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">size</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stride</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"Striding in slices not supported"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_twobit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tbf</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">stop</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tbf</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">do_mask</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__len__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_twobit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tbf</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">stop</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tbf</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">do_mask</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__len__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">end</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Trim start / stop</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,46 +41,47 @@ class TwoBitSequence( object ):</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">out_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">out_size</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"end before start (</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s,</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s)"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"end before start (</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s,</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s)"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Find position of packed portion</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">dna</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_twobit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tbf</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tbf</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">do_mask</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">dna</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_twobit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tbf</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tbf</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">do_mask</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Return</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dna</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TwoBitFile</span><span class="p">(</span> <span class="n" style="color: #333;">Mapping</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="n" style="color: #333;">do_mask</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TwoBitFile</span><span class="p">(</span><span class="n" style="color: #333;">Mapping</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="n" style="color: #333;">do_mask</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">do_mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">do_mask</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Read magic and determine byte order</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">byte_order</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">">"</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">strng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">TWOBIT_MAGIC_SIZE</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">magic</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unpack</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">">L"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">strng</span></span><span class="idiff right"> </span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">strng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">TWOBIT_MAGIC_SIZE</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">magic</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unpack</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">">L"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">strng</span></span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">magic</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">TWOBIT_MAGIC_NUMBER</span><span class="p">:</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">magic</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">TWOBIT_MAGIC_NUMBER_SWAP</span><span class="p">:</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">magic</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">TWOBIT_MAGIC_NUMBER_SWAP</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">byte_order</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<"</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"Not a NIB file"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"Not a NIB file"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">magic</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">magic</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Read version</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"L"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"L"</span></span><span class="p">)</span></span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">TWOBIT_VERSION</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"File is version '</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d' but I only know about '</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d'"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">version</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TWOBIT_VERSION</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"File is version '</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d' but I only know about '</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d'"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">version</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TWOBIT_VERSION</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Number of sequences in file</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"L"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"L"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Header contains some reserved space</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reserved</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"L"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reserved</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"L"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Read index of sequence names to offsets</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq_count</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">seq_count</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_p_string</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"L"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TwoBitSequence</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"L"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TwoBitSequence</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">offset</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__getitem__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__getitem__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">name</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loaded</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_sequence</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_sequence</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">name</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,42 +89,41 @@ class TwoBitFile( Mapping ):</td>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__len__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">load_sequence</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">load_sequence</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">name</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Seek to start of sequence block</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">header_offset</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">seq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">header_offset</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Size of sequence</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"L"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"L"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Read N and masked block regions</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_block_starts</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_block_sizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_block_coords</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">masked_block_starts</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">masked_block_sizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_block_coords</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Reserved</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"L"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"L"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Save start of actualt sequence</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tell</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Mark as loaded</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loaded</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_block_coords</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">blocks</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">block_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span> <span class="s" style="color: #d14;">"L"</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_block_coords</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">block_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="s" style="color: #d14;">"L"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">block_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[],</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">starts</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">block_count</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"L"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">untuple</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">sizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">block_count</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"L"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">untuple</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">starts</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sizes</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pattern</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">untuple</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">True</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">rval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unpack</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">byte_order</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pattern</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">read</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">calcsize</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">byte_order</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pattern</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">untuple</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">rval</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">starts</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">block_count</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"L"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">untuple</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">sizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">block_count</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"L"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">untuple</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">starts</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">sizes</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pattern</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">untuple</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">rval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unpack</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">byte_order</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pattern</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">read</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">calcsize</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">byte_order</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pattern</span></span><span class="p"><span class="idiff right">))</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">untuple</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">rval</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rval</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rval</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_p_string</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_p_string</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"><span class="s" style="color: #d14;"> Read a length-prefixed string<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;"> Read a length-prefixed string</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"B"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">length</span></span><span class="idiff right"> </span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"B"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">length</span></span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f"><strong>setup.cfg</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,9 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">snapshot = egg_info -rb_DEV bdist_egg rotate -m.egg -k1</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">build_docs = build_sphinx build_apidocs</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">[flake8]</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">ignore = E226,E501,E741</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">[nosetests]</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">tests=lib/, script_tests/</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">#verbosity=2</span>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/python-bx/compare/6f027516b60b06a62249ce405b98dbc87ac7a8cd...8ba7414e6c63650488dd76a932e6e4b3f10bc006#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +19,7 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"bx-python"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.8.<span class="idiff left right">2</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.8.<span class="idiff left right">4</span>"</span><span class="p">,</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">setup_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cython'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'six'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">py_modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">'psyco_full'</span> <span class="p">],</span></span>
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