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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-pyfaidx">Debian Med / python-pyfaidx</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/c5f6145c527ce3e11de8dee352bfa81444c9f53f">c5f6145c</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-17T22:26:06+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add patch to fix FTBFS
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/61cebfa0d11287674dbe2542d7fb3d023104784f">61cebfa0</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-17T22:30:00+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add B-D on python3-biopython
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/70aaa746684de9760cf2de337d73624a2dec164c">70aaa746</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-17T22:31:47+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Revert "Update patches"
This reverts commit 8c6f2831c1d107a5a6d8bb902672c4ba01f6ecf7.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/cf2d24aaa46dbdfce4b9336dfb801f514403dd28">cf2d24aa</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-17T22:33:57+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Properly re-diff locale patch
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#2380cdb4d7ba04fe48b0b05de58e69e1cbda4b95">
<span class="new-file">
+
debian/patches/fix-pkg-resources.patch
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</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#73930ea7cb72bccef0ed8b0eef9354cf13cbaffd">
<span class="new-file">
+
debian/patches/test-locale-to-c.patch
</span>
</a>
</li>
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/compare/707ff65c7f1d0a8320fa8dd428b0873f931c92f9...cf2d24aaa46dbdfce4b9336dfb801f514403dd28#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" 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="9" 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">@@ -9,6 +9,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<td class="new_line diff-line-num" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> python3-all,</span>
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<td class="new_line diff-line-num" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> python3-coverage,</span>
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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3-setuptools,</span>
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<td class="new_line diff-line-num new" data-linenumber="12" 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="LC12" class="line" lang="plaintext"> python3-biopython,</span>
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<td class="old_line diff-line-num" data-linenumber="12" 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="new_line diff-line-num" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> python3-numpy <!nocheck>,</span>
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<td class="old_line diff-line-num" data-linenumber="13" 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="new_line diff-line-num" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> python3-pkg-resources <!nocheck>,</span>
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<td class="new_line diff-line-num" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> python3-pytest <!nocheck>,</span>
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</li>
<li id="2380cdb4d7ba04fe48b0b05de58e69e1cbda4b95">
<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/compare/707ff65c7f1d0a8320fa8dd428b0873f931c92f9...cf2d24aaa46dbdfce4b9336dfb801f514403dd28#2380cdb4d7ba04fe48b0b05de58e69e1cbda4b95"><strong>debian/patches/fix-pkg-resources.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: pkg-resources only works once the package has been installed and breaks</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> in-place testing. Workaround it by making it n/a if not found</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2022-02-17</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pyfaidx/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pyfaidx/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -6,6 +6,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> from __future__ import division</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pkg_resources</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> import re</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> import string</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -25,8 +26,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> from collections import OrderedDict</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> except ImportError: #python 2.6</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> from ordereddict import OrderedDict</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-__version__ = get_distribution("pyfaidx").version</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+try:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ __version__ = get_distribution("pyfaidx").version</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+except (ImportError, pkg_resources.DistributionNotFound):</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ __version__ = 'n/a'</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> if sys.version_info > (3, ):</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> buffer = memoryview</span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/compare/707ff65c7f1d0a8320fa8dd428b0873f931c92f9...cf2d24aaa46dbdfce4b9336dfb801f514403dd28#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">test-locale-to-c.patch</span>
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1
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">remove-ignore-docstring.patch</span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">no_setuptools-scm.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">fix-pkg-resources.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/compare/707ff65c7f1d0a8320fa8dd428b0873f931c92f9...cf2d24aaa46dbdfce4b9336dfb801f514403dd28#73930ea7cb72bccef0ed8b0eef9354cf13cbaffd"><strong>debian/patches/test-locale-to-c.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Test locale to C</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Change the testing locale "C", for avoiding the case in which the</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> additional locale set "en_US.utf8" is not available.</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Sao I Kuan <saoikuan@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2020-09-30</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">--- a/tests/test_feature_indexing.py</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_feature_indexing.py</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -318,7 +318,7 @@</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import platform</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> if platform.system() == "Linux":</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- new_locale = 'en_US.utf8'</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ new_locale = 'C'</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> elif platform.system() == "Darwin":</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> new_locale = 'en_US.UTF-8'</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -349,4 +349,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> fasta_out.write("CTCCGGGCCCAT\nATAAAGCCTAAA\n")</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> faidx = Faidx(fasta_path)</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> finally:</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- shutil.rmtree(tmp_dir)</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ shutil.rmtree(tmp_dir)</span></span></pre>
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