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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-dnaio">Debian Med / python-dnaio</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/f30555526395dc7f296505f4fbe91e97bb4418b5">f3055552</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-08T13:16:36+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.4.3</pre>
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<h4>10 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#f75f54159d8ca95918e0cdbdcbc2012a7f8d47ed">
buildwheels.sh
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#38e7f48281a2602f08cb832d9472eb2330e11e51">
src/dnaio/__init__.py
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<li class="file-stats">
<a href="#79bba35b6cf4519cc3ab15da71893164d46ad480">
src/dnaio/readers.py
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<li class="file-stats">
<a href="#2c796bdd402f95103c9d6524cf0927843f28bec8">
src/dnaio/writers.py
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<a href="#307d17476eda4102236d69ec93ead958067e02d6">
tests/test_internal.py
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<li class="file-stats">
<a href="#ead909dd23c63486042d1782e7af8fd25690bbd7">
tests/test_open.py
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<li class="file-stats">
<a href="#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c">
tox.ini
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/f30555526395dc7f296505f4fbe91e97bb4418b5#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<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 +7,6 @@ cache:</td>
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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;">$HOME/.cache/pip</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;">python</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.4"</span></span>
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<td class="diff-line-num old_line" 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="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.5"</span></span>
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<td class="diff-line-num new_line" 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="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.7"</span></span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/f30555526395dc7f296505f4fbe91e97bb4418b5#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">@@ -4,7 +4,7 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="gh" style="color: #999;"># dnaio parses FASTQ and FASTA</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="sb" style="color: #d14;">`dnaio`</span> is a Python 3 library for fast parsing of FASTQ and also FASTA files. The code was previously part of the</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="sb" style="color: #d14;">`dnaio`</span> is a Python 3<span class="idiff left right">.5+</span> library for fast parsing of FASTQ and also FASTA files. The code was previously part of the</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Cutadapt</span><span class="p">](</span><span class="sx" style="color: #d14;">https://cutadapt.readthedocs.io/</span><span class="p">)</span> tool and has been improved since it has been split out.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<li id="f75f54159d8ca95918e0cdbdcbc2012a7f8d47ed">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/f30555526395dc7f296505f4fbe91e97bb4418b5#f75f54159d8ca95918e0cdbdcbc2012a7f8d47ed"><strong>buildwheels.sh</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Build manylinux<span class="idiff left right">1</span> wheels. Based on the example at</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Build manylinux wheels. Based on the example at</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <https://github.com/pypa/python-manylinux-demo></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># For interactive tests:</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># docker run -it -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># It is best to run this in a fresh clone of the repository!</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run this within the repository root:</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># ./buildwheels.sh</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The wheels will be put into the dist/ subdirectory.</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-xeuo</span> pipefail</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nv" style="color: #008080;">manylinux</span><span class="o" style="font-weight: 600;">=</span>quay.io/pypa/manylinux2010_x86_64</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># For convenience, if this script is called from outside of a docker container,</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># it starts a container and runs itself inside of it.</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> docker /proc/1/cgroup<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># We are not inside a container</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"> docker pull quay.io/pypa/manylinux1_x86_64</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exec </span>docker run <span class="nt" style="color: #000080;">--rm</span> <span class="nt" style="color: #000080;">-v</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span>:/io quay.io/pypa/manylinux1_x86_64 /io/<span class="nv" style="color: #008080;">$0</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> docker pull <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">manylinux</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exec </span>docker run <span class="nt" style="color: #000080;">--rm</span> <span class="nt" style="color: #000080;">-v</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span>:/io <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">manylinux</span><span class="k" style="font-weight: 600;">}</span> /io/<span class="nv" style="color: #008080;">$0</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-d</span> /io/dist<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> /io/dist</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">chown</span> <span class="nt" style="color: #000080;">--reference</span><span class="o" style="font-weight: 600;">=</span>/io/setup.py /io/dist</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Strip binaries (copied from multibuild)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="32" 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">@@ -21,21 +32,14 @@ STRIP_FLAGS=${STRIP_FLAGS:-"-Wl,-strip-all"}</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CFLAGS</span><span class="k" style="font-weight: 600;">:-</span><span class="nv" style="color: #008080;">$STRIP_FLAGS</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">CXXFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CXXFLAGS</span><span class="k" style="font-weight: 600;">:-</span><span class="nv" style="color: #008080;">$STRIP_FLAGS</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># We don’t support Python 2.7</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> /opt/python/cp27<span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"><span class="nv" style="color: #008080;">PYBINS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"/opt/python/*/bin"</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="nv" style="color: #008080;">HAS_CYTHON</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>PYBIN <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PYBINS</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PYBIN</span><span class="k" style="font-weight: 600;">}</span>/pip <span class="nb" style="color: #0086b3;">install </span>Cython</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># ${PYBIN}/pip install -r /io/requirements.txt</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PYBIN</span><span class="k" style="font-weight: 600;">}</span>/pip wheel /io/ <span class="nt" style="color: #000080;">-w</span> wheelhouse/</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>PYBIN <span class="k" style="font-weight: 600;">in</span> /opt/python/cp3[5678]-<span class="k" style="font-weight: 600;">*</span>/bin<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PYBIN</span><span class="k" style="font-weight: 600;">}</span>/pip wheel <span class="nt" style="color: #000080;">--no-deps</span> /io/ <span class="nt" style="color: #000080;">-w</span> wheelhouse/</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls </span>wheelhouse/</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Bundle external shared libraries into the wheels</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>whl <span class="k" style="font-weight: 600;">in </span>wheelhouse/<span class="idiff left right">dnaio-</span><span class="k" style="font-weight: 600;">*</span>.whl<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>auditwheel repair <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$whl</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-w</span> repaired/</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>whl <span class="k" style="font-weight: 600;">in </span>wheelhouse/<span class="k" style="font-weight: 600;">*</span>.whl<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>auditwheel repair <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$whl</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-<span class="idiff left">-plat</span></span><span class="idiff"> manylinux1_x86_64 </span><span class="nt" style="color: #000080;"><span class="idiff right">-</span>w</span> repaired/</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Created files are owned by root, so fix permissions.</span></span>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/f30555526395dc7f296505f4fbe91e97bb4418b5#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">@@ -4,8 +4,8 @@ from setuptools import setup, Extension, find_packages</td>
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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;">distutils.command.sdist</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sdist</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">_sdist</span></span>
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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;">distutils.command.build_ext</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">build_ext</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">_build_ext</span></span>
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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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[:</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">4</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Python 3.<span class="idiff left right">4</span> or later is required</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[:</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">5</span></span><span class="p">):</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Python 3.<span class="idiff left right">5</span> or later is required</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</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 class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</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>
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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">@@ -75,9 +75,9 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extensions</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;">cmdclass</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'build_ext'</span><span class="p">:</span> <span class="n" style="color: #333;">BuildExt</span><span class="p">,</span> <span class="s" style="color: #d14;">'sdist'</span><span class="p">:</span> <span class="n" style="color: #333;">SDist</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;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'xopen>=0.8.2'</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;">python_requires</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'>=3.<span class="idiff left right">4</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;">python_requires</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'>=3.<span class="idiff left right">5</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="s" style="color: #d14;">"Development Status :: <span class="idiff left right">4 - Beta</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="s" style="color: #d14;">"Development Status :: <span class="idiff left right">5 - Production/Stable</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="s" style="color: #d14;">"Intended Audience :: Science/Research"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">"License :: OSI Approved :: MIT License"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="s" style="color: #d14;">"Natural Language :: English"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/f30555526395dc7f296505f4fbe91e97bb4418b5#38e7f48281a2602f08cb832d9472eb2330e11e51"><strong>src/dnaio/__init__.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">@@ -128,6 +128,21 @@ def _detect_format_from_name(name):</td>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_is_path</span><span class="p">(</span><span class="n" style="color: #333;">obj</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"><span class="s" style="color: #d14;"> Return whether the given object looks like a path (str, pathlib.Path or pathlib2.Path)</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># pytest uses pathlib2.Path objects on Python 3.5 for its tmp_path fixture.</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># On Python 3.6+, this function can be replaced with isinstance(obj, os.PathLike)</span></span>
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<pre style="margin: 0;">+<span id="LC137" 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="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"pathlib2"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">modules</span><span class="p">:</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pathlib2</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">path_classes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">pathlib</span><span class="p">.</span><span class="n" style="color: #333;">Path</span><span class="p">,</span> <span class="n" style="color: #333;">pathlib2</span><span class="p">.</span><span class="n" style="color: #333;">Path</span><span class="p">)</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">path_classes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">pathlib</span><span class="p">.</span><span class="n" style="color: #333;">Path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">obj</span><span class="p">,</span> <span class="n" style="color: #333;">path_classes</span><span class="p">)</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"></span>
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_open_single</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="n" style="color: #333;">opener</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">fileformat</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"r"</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</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="LC147" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"><span class="s" style="color: #d14;"> Open a single sequence file. See description of open() above.</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">@@ -135,7 +150,7 @@ def _open_single(file, opener, *, fileformat=None, mode="r", qualities=None):</td>
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135
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mode</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"r"</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a"</span><span class="p">):</span></span>
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136
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Mode must be 'r', 'w' or 'a'"</span><span class="p">)</span></span>
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137
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">isinstance</span></span><span class="p"><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="p"><span class="idiff">(</span></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">pathlib</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Path</span></span><span class="p"><span class="idiff">)):</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># TODO Use os.PathLike in Python 3.6+</span></span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">_is_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="p"><span class="idiff right">):</span></span></span>
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139
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fspath</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>
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140
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opener</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"b"</span><span class="p">)</span></span>
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141
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">close_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</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">@@ -200,7 +215,8 @@ def _detect_format_from_content(file):</td>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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201
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">seekable</span><span class="p">():</span></span>
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202
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">first_char</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">tell</span><span class="p">()</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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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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204
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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205
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">first_char</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">formats</span> <span class="o" style="font-weight: 600;">=</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">@@ -228,6 +244,9 @@ class PairedSequenceReader:</td>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_close</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">pop_all</span><span class="p">().</span><span class="n" style="color: #333;">close</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">delivers_qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader1</span><span class="p">.</span><span class="n" style="color: #333;">delivers_qualities</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</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="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"PairedSequenceReader(file1={}, file2={})"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader1</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC250" 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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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"><span class="s" style="color: #d14;"> Iterate over the paired reads. Each item is a pair of Sequence objects.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="279" 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="298" 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">@@ -279,6 +298,9 @@ class InterleavedSequenceReader:</td>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_open_single</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">opener</span><span class="p">,</span> <span class="n" style="color: #333;">fileformat</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fileformat</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">delivers_qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader</span><span class="p">.</span><span class="n" style="color: #333;">delivers_qualities</span></span>
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</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="LC302" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"InterleavedSequenceReader({})"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC304" 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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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader</span><span class="p">)</span></span>
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="317" 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="339" 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">@@ -317,6 +339,9 @@ class PairedSequenceWriter:</td>
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">file2</span><span class="p">,</span> <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">opener</span><span class="p">,</span> <span class="n" style="color: #333;">fileformat</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fileformat</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mode</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qualities</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_close</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">pop_all</span><span class="p">().</span><span class="n" style="color: #333;">close</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</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="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"{}({}, {})"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span><span class="p">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_writer1</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_writer2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">):</span></span>
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_writer1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">)</span></span>
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_writer2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read2</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="347" 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="372" 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">@@ -347,6 +372,9 @@ class InterleavedSequenceWriter:</td>
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347
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_open_single</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">opener</span><span class="p">,</span> <span class="n" style="color: #333;">fileformat</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fileformat</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mode</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</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="LC376" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"{}({})"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span><span class="p">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_writer</span><span class="p">)</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"></span>
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350
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">):</span></span>
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351
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_writer</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">)</span></span>
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352
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_writer</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read2</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/f30555526395dc7f296505f4fbe91e97bb4418b5#79bba35b6cf4519cc3ab15da71893164d46ad480"><strong>src/dnaio/readers.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" 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">@@ -30,6 +30,9 @@ class BinaryFileReader:</td>
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_close_on_exit</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span></span>
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32
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32
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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;">__repr__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="34" 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">
34
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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="s" style="color: #d14;">"{}({!r})"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span><span class="p">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</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;">close</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="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_close_on_exit</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/f30555526395dc7f296505f4fbe91e97bb4418b5#2c796bdd402f95103c9d6524cf0927843f28bec8"><strong>src/dnaio/writers.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,9 @@ class FileWriter:</td>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_close_on_exit</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">(</span><span class="n" style="color: #333;">_close_file</span><span class="p">)</span></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"{}({!r})"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span><span class="p">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</span><span class="p">))</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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16
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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;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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14
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_close_on_exit</span><span class="p">:</span></span>
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15
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18
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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="p">.</span><span class="n" style="color: #333;">_file</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" 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="39" 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">@@ -36,6 +39,9 @@ class FastaWriter(FileWriter):</td>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">opener</span><span class="p">,</span> <span class="n" style="color: #333;">_close_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_close_file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">line_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_length</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line_length</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</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="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"FastaWriter({!r})"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name_or_record</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</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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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"""Write an entry to the the FASTA file.</span></span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/f30555526395dc7f296505f4fbe91e97bb4418b5#307d17476eda4102236d69ec93ead958067e02d6"><strong>tests/test_internal.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">@@ -324,8 +324,6 @@ class TestInterleavedReader:</td>
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324
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="p">]</span></span>
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">InterleavedSequenceReader</span><span class="p">(</span><span class="s" style="color: #d14;">"tests/data/interleaved.fastq"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">isr</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">isr</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">e1</span><span class="p">,</span> <span class="n" style="color: #333;">e2</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">reads</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="n" style="color: #333;">e1</span><span class="p">,</span> <span class="n" style="color: #333;">e2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">reads</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"tests/data/interleaved.fastq"</span><span class="p">,</span> <span class="n" style="color: #333;">interleaved</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/f30555526395dc7f296505f4fbe91e97bb4418b5#ead909dd23c63486042d1782e7af8fd25690bbd7"><strong>tests/test_open.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">@@ -49,6 +49,20 @@ def test_version():</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="n" style="color: #333;">__version__</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>
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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;">test_open_nonexistent</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">FileNotFoundError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"nonexistent"</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;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"></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 class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_open_empty_file_with_unrecognized_extension</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"unrecognized-extension.tmp"</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">touch</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;">with</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</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 class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></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_read</span><span class="p">(</span><span class="n" style="color: #333;">fileformat</span><span class="p">,</span> <span class="n" style="color: #333;">extension</span><span class="p">):</span></span>
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53
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"tests/data/simple."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fileformat</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">extension</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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54
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/f30555526395dc7f296505f4fbe91e97bb4418b5#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c"><strong>tox.ini</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="ini"><span class="nn" style="color: #555;">[tox]</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="ini"><span class="py">envlist</span> <span class="p">=</span> <span class="s" style="color: #d14;">flake8,py3<span class="idiff left right">4,py3</span>5,py36,py37,py38</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="ini"><span class="py">envlist</span> <span class="p">=</span> <span class="s" style="color: #d14;">flake8,py35,py36,py37,py38</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="ini"></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="ini"><span class="nn" style="color: #555;">[testenv]</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="ini"><span class="py">deps</span> <span class="p">=</span></span>
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