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GitLab

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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/00964d9fc99ded67eb43eb39c9d8f4c745c1076e">00964d9f</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-10-03T03:40:03+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.6.0</pre>

</li>

</ul>

<h4>17 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#899ce9c202bf7bb5480e72836c3edc773c9c4244">

.github/workflows/ci.yml

</a>

</li>

<li class="file-stats">

<a href="#4990be809a537bf86e4be2fe2e8251c83d8bd129">

CHANGES.rst

</a>

</li>

<li class="file-stats">

<a href="#8875df48c18030126ef5ef5a6f5c93b23451fb9f">

MANIFEST.in

</a>

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<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

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<li class="file-stats">

<a href="#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491">

pyproject.toml

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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

</a>

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<li class="file-stats">

<a href="#324fa7612afdef67bd89878b1541ef5f20718be0">

src/dnaio/_core.pyi

</a>

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<li class="file-stats">

<a href="#72ff21bf4040f97f9c5919d676e807b4117d01b7">

src/dnaio/_core.pyx

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<li class="file-stats">

<a href="#e5795f7640126a0eb096e91cf0373d32d878161f">

src/dnaio/_util.py

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<a href="#176822612ada6c351a79b7da6087bb1f3e38c551">

src/dnaio/exceptions.py

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<a href="#7af161688a569301ddcba97224af13ce910580cc">

<span class="new-file">

+

src/dnaio/interfaces.py

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</li>

<li class="file-stats">

<a href="#a66e9807f4b39aaa61baab58ad1a281bd6691999">

<span class="new-file">

+

src/dnaio/pairedend.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="#09b1291e3cfc7a40be592455cb1acaacfa12b950">

<span class="new-file">

+

src/dnaio/singleend.py

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<li class="file-stats">

<a href="#2c796bdd402f95103c9d6524cf0927843f28bec8">

src/dnaio/writers.py

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<li class="file-stats">

<a href="#307d17476eda4102236d69ec93ead958067e02d6">

tests/test_internal.py

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</ul>

<h4>Changes:</h4>

<li id="899ce9c202bf7bb5480e72836c3edc773c9c4244">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#899ce9c202bf7bb5480e72836c3edc773c9c4244"><strong>.github/workflows/ci.yml</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" 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="26" 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">@@ -26,7 +26,7 @@ jobs:</td>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml">    <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.os }}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml">    <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="28" 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="LC28" class="line" lang="yaml">      <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml">        <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">3.6</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.7</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.8</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.9</span><span class="pi">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml">        <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">3.6</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.7</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.8</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.9</span><span class="pi"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="s" style="color: #d14;"><span class="idiff right">3.10-dev"</span></span><span class="pi">]</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="yaml">        <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">ubuntu-latest</span><span class="pi">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml">        <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>

</pre>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="yaml">        <span class="pi">-</span> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="m" style="color: #099;">3.8</span></span>

</pre>

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<br>

</li>

<li id="4990be809a537bf86e4be2fe2e8251c83d8bd129">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#4990be809a537bf86e4be2fe2e8251c83d8bd129"><strong>CHANGES.rst</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2" 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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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Changelog</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">=========</span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">v0.6.0 (2021-09-28)</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">-------------------</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="8" 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">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="9" 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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">* PR #12: Improve FASTQ writing speed twofold (thanks to @rhpvorderman)</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="10" 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">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>

</pre>

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11

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">v0.5.2 (2021-09-07)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">-------------------</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8875df48c18030126ef5ef5a6f5c93b23451fb9f">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#8875df48c18030126ef5ef5a6f5c93b23451fb9f"><strong>MANIFEST.in</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="old_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">include README.md</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2" 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">

2

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<td class="new_line diff-line-num" data-linenumber="2" 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">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">include LICENSE</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">include src/dnaio/*.c</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="new_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">include versioneer.py</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="new_line diff-line-num" data-linenumber="4" 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">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">include src/dnaio/_version.py</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" 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="34" 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">@@ -34,7 +34,7 @@ The main interface is the `dnaio.open` function:</td>

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34

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34

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>

</pre>

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35

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35

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Limitations</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

36

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<td class="new_line diff-line-num" 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">

36

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

37

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<td class="new_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"><span class="p">-</span> Multi-line FASTQ files are not supported.<span class="idiff left right"> You shouldn’t use them anyway.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="38" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="37" 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">

37

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="p">-</span> Multi-line FASTQ files are not supported.</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="38" 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">

38

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<td class="new_line diff-line-num" data-linenumber="38" 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">

38

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"><span class="p">-</span> FASTQ parsing is the focus of this library. The FASTA parser is not as optimized.</span>

</pre>

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<td class="old_line diff-line-num" 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">

39

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<td class="new_line diff-line-num" 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">

39

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"></span>

</pre>

</td>

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40

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40

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"></span>

</pre>

</td>

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<br>

</li>

<li id="5d07e7d72637aa0d59c89d381fe6dc4cf46e2491">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491"><strong>pyproject.toml</strong></a>

<hr>

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<td class="old_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="toml"><span class="nn" style="color: #555;">[build-system]</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2" 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">

2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="toml"><span class="py">requires</span> <span class="p">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"setuptools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"wheel"</span><span class="p">,</span> <span class="s" style="color: #d14;">"setuptools_scm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Cython"</span><span class="p">]</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="toml"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="toml"><span class="nn" style="color: #555;">[black.tool]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" 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">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="toml"><span class="py">line-length</span> <span class="p">=</span> <span class="mi" style="color: #099;">100</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

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<td class="old_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2" 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">

2

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<td class="new_line diff-line-num" data-linenumber="2" 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">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span><span class="p">,</span> <span class="n" style="color: #333;">Extension</span><span class="p">,</span> <span class="n" style="color: #333;">find_packages</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" 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="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_sdist</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" 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="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_build_ext</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="5" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" 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>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="5" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">no_cythonize</span><span class="p">(</span><span class="n" style="color: #333;">extensions</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">_ignore</span><span class="p">):</span></span>

</pre>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" 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="20" 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">@@ -20,18 +20,13 @@ def no_cythonize(extensions, **_ignore):</td>

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<td class="new_line diff-line-num" data-linenumber="20" 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="LC20" class="line" lang="python">        <span class="n" style="color: #333;">extension</span><span class="p">.</span><span class="n" style="color: #333;">sources</span><span class="p">[:]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sources</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python">    <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">'dnaio._core'</span><span class="p">,</span> <span class="n" style="color: #333;">sources</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'src/dnaio/_core.pyx'</span><span class="p">]),</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BuildExt</span><span class="p">(</span><span class="n" style="color: #333;">_build_ext</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BuildExt</span><span class="p">(</span><span class="n" style="color: #333;">build_ext</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="29" 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="LC24" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># If we encounter a PKG-INFO file, then this is likely a .tar.gz/.zip</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="26" 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="LC26" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># file retrieved from PyPI that already includes the pre-cythonized</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" data-linenumber="27" 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="LC27" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># extension modules, and then we do not need to run cythonize().</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">'PKG-INFO'</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python">            <span class="n" style="color: #333;">no_cythonize</span><span class="p">(</span><span class="n" style="color: #333;">extensions</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">            <span class="n" style="color: #333;">no_cythonize</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">extensions</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Otherwise, this is a 'developer copy' of the code, and then the</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="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">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># only sensible thing is to require Cython to be installed.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" 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="35" 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">@@ -40,11 +35,11 @@ class BuildExt(_build_ext):</td>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SDist</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>sdist</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SDist</span><span class="p">(</span><span class="n" style="color: #333;">sdist</span><span class="p">):</span></span>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<td class="new_line diff-line-num" data-linenumber="40" 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="LC40" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Make sure the compiled Cython files in the distribution are up-to-date</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python">        <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Cython.Build</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cythonize</span></span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python">        <span class="n" style="color: #333;">cythonize</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">extension</span>s</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python">        <span class="n" style="color: #333;">cythonize</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">distribution</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">ext_module</span>s</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">run</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>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" 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">@@ -58,7 +53,7 @@ setup(</td>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python">    <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Marcel Martin'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python">    <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'marcel.martin@scilifelab.se'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python">    <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'https://github.com/marcelm/dnaio/'</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python">    <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Read FASTA and FASTQ files efficiently'</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python">    <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Read <span class="idiff left right">and write </span>FASTA and FASTQ files efficiently'</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python">    <span class="n" style="color: #333;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">long_description</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="63" 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="LC58" class="line" lang="python">    <span class="n" style="color: #333;">long_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'text/markdown'</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;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'MIT'</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">@@ -68,7 +63,9 @@ setup(</td>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python">    <span class="n" style="color: #333;">extras_require</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 class="s" style="color: #d14;">'dev'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'Cython'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pytest'</span><span class="p">],</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python">    <span class="p">},</span></span>

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<pre style="margin: 0;">-<span id="LC71" 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="LC66" class="line" lang="python">    <span class="n" style="color: #333;">ext_modules</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python">        <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">'dnaio._core'</span><span class="p">,</span> <span class="n" style="color: #333;">sources</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'src/dnaio/_core.pyx'</span><span class="p">]),</span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python">    <span class="p">],</span></span>

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<pre style="margin: 0;"> <span id="LC69" 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="LC70" 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="LC71" 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;">'>=3.6'</span><span class="p">,</span></span>

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<br>

</li>

<li id="38e7f48281a2602f08cb832d9472eb2330e11e51">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#38e7f48281a2602f08cb832d9472eb2330e11e51"><strong>src/dnaio/__init__.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,6 +5,10 @@ Sequence I/O: Read and write FASTA and FASTQ files efficiently</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python">    <span class="s" style="color: #d14;">'open'</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python">    <span class="s" style="color: #d14;">'Sequence'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python">    <span class="s" style="color: #d14;">'SingleEndReader'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python">    <span class="s" style="color: #d14;">'PairedEndReader'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="10" 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">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="python">    <span class="s" style="color: #d14;">'SingleEndWriter'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="8" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" 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">

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="python">    <span class="s" style="color: #d14;">'PairedEndWriter'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12" class="line" lang="python">    <span class="s" style="color: #d14;">'FastaReader'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="python">    <span class="s" style="color: #d14;">'FastaWriter'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">    <span class="s" style="color: #d14;">'FastqReader'</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" 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">@@ -13,30 +17,35 @@ __all__ = [</td>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="new_line diff-line-num" data-linenumber="17" 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">

17

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC17" class="line" lang="python">    <span class="s" style="color: #d14;">'FileFormatError'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="new_line diff-line-num" data-linenumber="18" 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">

18

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC18" class="line" lang="python">    <span class="s" style="color: #d14;">'FastaFormatError'</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="new_line diff-line-num" data-linenumber="19" 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">

19

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">    <span class="s" style="color: #d14;">'FastqFormatError'</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="new_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="python">    <span class="s" style="color: #d14;">'InterleavedSequenceReader'</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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<td class="new_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="python">    <span class="s" style="color: #d14;">'InterleavedSequenceWriter'</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

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<td class="new_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="python">    <span class="s" style="color: #d14;">'PairedSequenceReader'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="19" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="20" 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">

20

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">    <span class="s" style="color: #d14;">'InterleavedPairedEndReader'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="19" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="21" 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">

21

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">    <span class="s" style="color: #d14;">'InterleavedPairedEndWriter'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="19" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="22" 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">

22

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">    <span class="s" style="color: #d14;">'TwoFilePairedEndReader'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="19" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="23" 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">

23

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">    <span class="s" style="color: #d14;">'TwoFilePairedEndWriter'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="19" 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">

19

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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC24" class="line" lang="python">    <span class="s" style="color: #d14;">'read_chunks'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="20" 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">

20

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<td class="new_line diff-line-num" data-linenumber="25" 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">

25

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC25" class="line" lang="python">    <span class="s" style="color: #d14;">'read_paired_chunks'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" 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">

21

</td>

<td class="new_line diff-line-num" data-linenumber="26" 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">

26

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC26" class="line" lang="python">    <span class="s" style="color: #d14;">'record_names_match'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<td class="new_line diff-line-num" data-linenumber="27" 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">

27

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC27" class="line" lang="python">    <span class="s" style="color: #d14;">'__version__'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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<td class="new_line diff-line-num" data-linenumber="28" 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">

28

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="p">]</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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<td class="new_line diff-line-num" data-linenumber="29" 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">

29

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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<td class="new_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

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<td class="new_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fspath</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

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<td class="new_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">contextlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ExitStack</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

28

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<td class="new_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">functools</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

29

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<td class="new_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">typing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Optional</span><span class="p">,</span> <span class="n" style="color: #333;">Union</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">,</span> <span class="n" style="color: #333;">Tuple</span><span class="p">,</span> <span class="n" style="color: #333;">Iterator</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="30" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="30" 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">

30

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PathLike</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="30" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="31" 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">

31

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">typing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Optional</span><span class="p">,</span> <span class="n" style="color: #333;">Union</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" 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">

30

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<td class="new_line diff-line-num" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="31" 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">

31

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<td class="new_line diff-line-num" data-linenumber="33" 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">

33

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">xopen</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">xopen</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

32

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="33" 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">

33

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<td class="new_line diff-line-num" data-linenumber="35" 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">

35

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">record_names_match</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="34" 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">

34

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<td class="new_line diff-line-num" 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">

36

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.readers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastqReader</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="35" 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">

35

</td>

<td class="new_line diff-line-num" data-linenumber="37" 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">

37

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.writers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="36" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="38" 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">

38

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.singleend</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_open_single</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="36" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="39" 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">

39

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.pairedend</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="36" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="40" 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">

40

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC40" class="line" lang="python">    <span class="n" style="color: #333;">TwoFilePairedEndReader</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="36" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="41" 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">

41

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC41" class="line" lang="python">    <span class="n" style="color: #333;">TwoFilePairedEndWriter</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="36" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="42" 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">

42

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC42" class="line" lang="python">    <span class="n" style="color: #333;">InterleavedPairedEndReader</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python">    <span class="n" style="color: #333;">InterleavedPairedEndWriter</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="p">)</span></span>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" data-linenumber="45" 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="LC45" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">UnknownFileFormat</span><span class="p">,</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">,</span> <span class="n" style="color: #333;">FastaFormatError</span><span class="p">,</span> <span class="n" style="color: #333;">FastqFormatError</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.interfaces</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SingleEndReader</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndReader</span><span class="p">,</span> <span class="n" style="color: #333;">SingleEndWriter</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndWriter</span></span>

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<td class="new_line diff-line-num" data-linenumber="47" 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="LC47" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.chunks</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">read_chunks</span><span class="p">,</span> <span class="n" style="color: #333;">read_paired_chunks</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">version</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">__version__</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_is_path</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="49" 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="LC49" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="51" 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="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" 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="58" 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">@@ -49,46 +58,45 @@ def open(</td>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python">    <span class="n" style="color: #333;">qualities</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">]</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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<td class="new_line diff-line-num" data-linenumber="59" 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="LC59" class="line" lang="python">    <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Union</span><span class="p">[</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python">    <span class="n" style="color: #333;">FastaReader</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python">    <span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC54" class="line" lang="python">    <span class="n" style="color: #333;">FastqReader</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python">    <span class="n" style="color: #333;">FastqWriter</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python">    <span class="s" style="color: #d14;">"PairedSequenceReader"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python">    <span class="s" style="color: #d14;">"PairedSequenceWriter"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python">    <span class="s" style="color: #d14;">"PairedSequenceAppender"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python">    <span class="s" style="color: #d14;">"InterleavedSequenceReader"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python">    <span class="s" style="color: #d14;">"InterleavedSequenceWriter"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python">    <span class="s" style="color: #d14;">"InterleavedSequenceAppender"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python">    <span class="n" style="color: #333;">SingleEndReader</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python">    <span class="n" style="color: #333;">PairedEndReader</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python">    <span class="n" style="color: #333;">SingleEndWriter</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python">    <span class="n" style="color: #333;">PairedEndWriter</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"><span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;">    Open sequence files in FASTA or FASTQ format for reading or writing. This is</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"><span class="s" style="color: #d14;">    a factory that returns an instance of one of the ...Reader or ...Writer</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;">    classes also defined in this module.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;">    Open sequence files in FASTA or FASTQ format for reading or writing.</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="68" 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="LC68" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"><span class="s" style="color: #d14;">    file1, file2 -- Paths to regular or compressed files or file-like</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"><span class="s" style="color: #d14;">    Parameters:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"><span class="s" style="color: #d14;">      file1:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"><span class="s" style="color: #d14;">      file2:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"><span class="s" style="color: #d14;">        Paths to regular or compressed files or file-like</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"><span class="s" style="color: #d14;">        objects (as str or as pathlib.Path). Use only file1 if data is single-end.</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;">        If sequences are paired, use also file2.</span></span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"><span class="s" style="color: #d14;">    <span class="idiff left right">mode --</span> Either 'r' for reading, 'w' for writing or 'a' for appending.</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;">    <span class="idiff left right">interleaved --</span> If True, then file1 contains interleaved paired-end data.</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="s" style="color: #d14;">      mode:</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"><span class="s" style="color: #d14;">    <span class="idiff left">   </span> Either <span class="idiff">``</span>'r'<span class="idiff">``</span> for reading, <span class="idiff">``</span>'w'<span class="idiff">``</span> for writing or <span class="idiff">``</span>'a'<span class="idiff right">``</span> for appending.</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="s" style="color: #d14;">      interleaved:</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"><span class="s" style="color: #d14;">    <span class="idiff left right">   </span> If True, then file1 contains interleaved paired-end data.</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"><span class="s" style="color: #d14;">        file2 must be None in this case.</span></span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"><span class="s" style="color: #d14;">    fileformat -- If set to None, the file format is autodetected from the file name</span></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"><span class="s" style="color: #d14;">        extension. Set to 'fasta' or 'fastq' to not auto-detect.</span></span>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;">    qualities -- When mode is 'w' and fileformat is None, this can be set to</span></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"><span class="s" style="color: #d14;">        True or False to specify whether the written sequences will have quality</span></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"><span class="s" style="color: #d14;">        values. This is is used in two ways:</span></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;">        * If the output format cannot be determined (unrecognized extension</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;">      fileformat:</span></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"><span class="s" style="color: #d14;">        If *None*, the file format is autodetected from the file name</span></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"><span class="s" style="color: #d14;">        extension. Set to ``'fasta'`` or ``'fastq'`` to not auto-detect.</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;">      qualities:</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;">        When mode is ``'w'`` and fileformat is *None*, this can be set</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="s" style="color: #d14;">        to *True* or *False* to specify whether the written sequences will have</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"><span class="s" style="color: #d14;">        quality values. This is is used in two ways:</span></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"><span class="s" style="color: #d14;">        - If the output format cannot be determined (unrecognized extension</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;">          etc), no exception is raised, but fasta or fastq format is chosen</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;">          appropriately.</span></span>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"><span class="s" style="color: #d14;">        * When False (no qualities available), an exception is raised when the</span></span>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"><span class="s" style="color: #d14;">          auto-detected output format is FASTQ.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;">    opener -- A function that is used to open file1 and file2 if they are not</span></span>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;">        already open file-like objects. By default, xopen is used, which can</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;">        - When False (no qualities available), an exception is raised when the</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;">          auto-detected output format is FASTQ.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;">      opener: A function that is used to open file1 and file2 if they are not</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="s" style="color: #d14;">        already open file-like objects. By default, ``xopen`` is used, which can</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;">        also open compressed file formats.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;">    Return:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;">       An instance of one of the ...Reader or ...Writer classes</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC101" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC102" 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>

</pre>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="107" 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">@@ -99,328 +107,19 @@ def open(</td>

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<pre style="margin: 0;"> <span id="LC107" 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;">in</span> <span class="s" style="color: #d14;">"wa"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">file1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">file2</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC108" 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;">"The paired-end output files are identical"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</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>

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<td class="new_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">PairedSequence</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="p">,</span> <span class="n" style="color: #333;">fileformat</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>

</pre>

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python">        <span class="k" style="font-weight: 600;"><span class="idiff left">elif</span></span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"<span class="idiff">w"</span></span><span class="p"><span class="idiff right">:</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python">        <span class="idiff left">    </span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff">PairedSequenceWriter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">file1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">file2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fileformat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qualities</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opener</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">opener</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python">        <span class="k" style="font-weight: 600;"><span class="idiff left">else</span></span><span class="p"><span class="idiff right">:</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python">        <span class="idiff left">    </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PairedSequenceAppender</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">file1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">file2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fileformat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qualities</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opener</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">opener</span></span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">TwoFilePairedEnd</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">fileformat</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="n" style="color: #333;">fileformat</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>

</pre>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left">append</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"<span class="idiff right">a"</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">TwoFilePairedEndWriter</span></span><span class="p"><span class="idiff right">(</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="113" 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">

113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python">        <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">file1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">file2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fileformat</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">fileformat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qualities</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">qualities</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opener</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">opener</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">append</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python">        <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="115" 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="LC115" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">interleaved</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="116" 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="LC116" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">InterleavedSequenceReader</span><span class="p">(</span><span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">fileformat</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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

110

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<td class="new_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"w"</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

111

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<td class="new_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">InterleavedSequenceWriter</span><span class="p">(</span><span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">fileformat</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">InterleavedSequenceAppender</span><span class="p">(</span><span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">fileformat</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="117" 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">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">InterleavedPairedEndReader</span><span class="p">(</span><span class="n" style="color: #333;">file1</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;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">opener</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python">        <span class="n" style="color: #333;">append</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"a"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="119" 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">

119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">InterleavedPairedEndWriter</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python">            <span class="n" style="color: #333;">file1</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;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qualities</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;">append</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">append</span><span class="p">)</span></span>

</pre>

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114

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<td class="new_line diff-line-num" data-linenumber="121" 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="LC121" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># The multi-file options have been dealt with, delegate rest to the</span></span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># single-file function.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</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="LC125" class="line" lang="python">        <span class="n" style="color: #333;">file1</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="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></pre>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_detect_format_from_name</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]:</span></span>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"><span class="s" style="color: #d14;">    name -- file name</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;">    Return 'fasta', 'fastq' or None if the format could not be detected.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python">    <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ext</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'.gz'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.xz'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.bz2'</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="n" style="color: #333;">ext</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python">            <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">ext</span><span class="p">)]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python">            <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python">    <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ext</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.fa'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.fna'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.csfasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.csfa'</span><span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'fasta'</span></span>

</pre>

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135

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">ext</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.fq'</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'.txt'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'_sequence'</span><span class="p">)):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'fastq'</span></span>

</pre>

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137

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC140" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python">    <span class="n" style="color: #333;">file_or_path</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python">    <span class="n" style="color: #333;">opener</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python">    <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python">    <span class="n" style="color: #333;">fileformat</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python">    <span class="n" style="color: #333;">mode</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"r"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python">    <span class="n" style="color: #333;">qualities</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="n" style="color: #333;">FastaReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span><span class="p">]:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;">    Open a single sequence file. See description of open() above.</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC151" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC152" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python">    <span class="n" style="color: #333;">path</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_is_path</span><span class="p">(</span><span class="n" style="color: #333;">file_or_path</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC156" 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="n" style="color: #333;">file_or_path</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># type: ignore</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC157" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC158" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</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="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">file_or_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'readinto'</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC161" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python">                <span class="s" style="color: #d14;">'When passing in an open file-like object, it must have been opened in binary mode'</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC163" 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;">file_or_path</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python">            <span class="n" style="color: #333;">path</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;">name</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python">            <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC168" 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;">False</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python">    <span class="n" style="color: #333;">fastq_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastqReader</span> <span class="k" style="font-weight: 600;">if</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="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">FastqWriter</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python">    <span class="n" style="color: #333;">fasta_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaReader</span> <span class="k" style="font-weight: 600;">if</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="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">FastaWriter</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

171

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python">    <span class="n" style="color: #333;">handlers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

172

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python">        <span class="s" style="color: #d14;">'fastq'</span><span class="p">:</span> <span class="n" style="color: #333;">functools</span><span class="p">.</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">fastq_handler</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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python">        <span class="s" style="color: #d14;">'fasta'</span><span class="p">:</span> <span class="n" style="color: #333;">functools</span><span class="p">.</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">fasta_handler</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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

174

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileformat</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

176

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python">            <span class="n" style="color: #333;">handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">handlers</span><span class="p">[</span><span class="n" style="color: #333;">fileformat</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python">            <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">UnknownFileFormat</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python">                <span class="s" style="color: #d14;">"File format {!r} is unknown (expected 'fasta' or 'fastq')."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">fileformat</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">handler</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_detect_format_from_name</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileformat</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'w'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">qualities</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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Format not recognized, but we know whether to use a format with or without qualities</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

188

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'fastq'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qualities</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'fasta'</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</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="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">fileformat</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_detect_format_from_content</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileformat</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

193

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python">            <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python">            <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">UnknownFileFormat</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python">                <span class="s" style="color: #d14;">'Could not determine whether file "{}" is FASTA or FASTQ. The file extension was '</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python">                <span class="s" style="color: #d14;">'not available or not recognized and the first character in the file is '</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python">                <span class="s" style="color: #d14;">'unexpected.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileformat</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'w'</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python">        <span class="n" style="color: #333;">extra</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" because the output file name is not available"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">UnknownFileFormat</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python">            <span class="s" style="color: #d14;">"Auto-detection of the output file format (FASTA/FASTQ) failed"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">extra</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileformat</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'fastq'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">mode</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"wa"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">qualities</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC209" 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>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python">            <span class="s" style="color: #d14;">'Output format cannot be FASTQ since no quality values are available.'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">handlers</span><span class="p">[</span><span class="n" style="color: #333;">fileformat</span><span class="p">](</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_detect_format_from_content</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"><span class="s" style="color: #d14;">    Return 'fasta', 'fastq' or None</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC219" 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>

</pre>

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<pre style="margin: 0;">-<span id="LC220" 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>

</pre>

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<pre style="margin: 0;">-<span id="LC221" 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>

</pre>

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<pre style="margin: 0;">-<span id="LC222" 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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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC224" 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 class="c1" style="color: #998; font-style: italic;"># type: ignore</span></span>

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<pre style="margin: 0;">-<span id="LC225" 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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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python">        <span class="sa">b</span><span class="s" style="color: #d14;">'@'</span><span class="p">:</span> <span class="s" style="color: #d14;">'fastq'</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python">        <span class="sa">b</span><span class="s" style="color: #d14;">'>'</span><span class="p">:</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python">        <span class="sa">b</span><span class="s" style="color: #d14;">'#'</span><span class="p">:</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;"># Some FASTA variants allow comments</span></span>

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<td class="old_line diff-line-num old" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python">        <span class="sa">b</span><span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="s" style="color: #d14;">'fastq'</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;"># Pretend FASTQ for empty input</span></span>

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">formats</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">first_char</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedSequenceReader</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"><span class="s" style="color: #d14;">    Read paired-end reads from two files.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"><span class="s" style="color: #d14;">    Wraps two BinaryFileReader instances, making sure that reads are properly</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"><span class="s" style="color: #d14;">    paired.</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python">    <span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python">        <span class="n" style="color: #333;">file1</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python">        <span class="n" style="color: #333;">file2</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</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="LC248" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python">    <span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">ExitStack</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">stack</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader1</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;">enter_context</span><span class="p">(</span><span class="n" style="color: #333;">_open_single</span><span class="p">(</span><span class="n" style="color: #333;">file1</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>

</pre>

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader2</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;">enter_context</span><span class="p">(</span><span class="n" style="color: #333;">_open_single</span><span class="p">(</span><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>

</pre>

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<pre style="margin: 0;">-<span id="LC253" 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>

</pre>

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<pre style="margin: 0;">-<span id="LC254" 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>

</pre>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC256" 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 class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC257" 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="LC258" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC259" 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 class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Iterator</span><span class="p">[</span><span class="n" style="color: #333;">Tuple</span><span class="p">[</span><span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="p">]]:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC261" 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>

</pre>

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Avoid usage of zip() below since it will consume one item too many.</span></span>

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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python">        <span class="n" style="color: #333;">it1</span><span class="p">,</span> <span class="n" style="color: #333;">it2</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;">reader1</span><span class="p">),</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;">reader2</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python">                <span class="n" style="color: #333;">r1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">it1</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">StopIteration</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># End of file 1. Make sure that file 2 is also at end.</span></span>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">it2</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python">                        <span class="s" style="color: #d14;">"Reads are improperly paired. There are more reads in "</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python">                        <span class="s" style="color: #d14;">"file 2 than in file 1."</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">StopIteration</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python">                    <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python">                <span class="n" style="color: #333;">r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">it2</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">StopIteration</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python">                    <span class="s" style="color: #d14;">"Reads are improperly paired. There are more reads in "</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python">                    <span class="s" style="color: #d14;">"file 1 than in file 2."</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">record_names_match</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">(</span></span>

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python">                    <span class="s" style="color: #d14;">"Reads are improperly paired. Read name '{}' "</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python">                    <span class="s" style="color: #d14;">"in file 1 does not match '{}' in file 2."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</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>

</pre>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC290" 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 class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC291" 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="p">()</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__enter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__exit__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exc</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC297" 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="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">InterleavedSequenceReader</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"><span class="s" style="color: #d14;">    Read paired-end reads from an interleaved FASTQ file.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python">    <span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python">    <span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python">        <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>

</pre>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">reader</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">FastaReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastqReader</span><span class="p">))</span>  <span class="c1" style="color: #998; font-style: italic;"># for Mypy</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC314" 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;">reader</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC315" 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>

</pre>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC317" 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 class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC318" 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>

</pre>

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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC320" 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 class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Iterator</span><span class="p">[</span><span class="n" style="color: #333;">Tuple</span><span class="p">[</span><span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="p">]]:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC321" 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>

</pre>

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<pre style="margin: 0;">-<span id="LC322" 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>

</pre>

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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python">                <span class="n" style="color: #333;">r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">StopIteration</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python">                    <span class="s" style="color: #d14;">"Interleaved input file incomplete: Last record "</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python">                    <span class="s" style="color: #d14;">"{!r} has no partner."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">record_names_match</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python">                    <span class="s" style="color: #d14;">"Reads are improperly paired. Name {!r} "</span></span>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python">                    <span class="s" style="color: #d14;">"(first) does not match {!r} (second)."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="n" style="color: #333;">line</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="LC333" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</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>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC335" 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 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="LC336" 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="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__enter__</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="LC339" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__exit__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC342" 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="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedSequenceWriter</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python">    <span class="n" style="color: #333;">_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"w"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC347" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python">        <span class="n" style="color: #333;">file1</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python">        <span class="n" style="color: #333;">file2</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"fastq"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python">        <span class="n" style="color: #333;">qualities</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python">    <span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">ExitStack</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">stack</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC357" 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;">Union</span><span class="p">[</span><span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC358" 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;">Union</span><span class="p">[</span><span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC359" 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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">enter_context</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python">                <span class="n" style="color: #333;">_open_single</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python">                    <span class="n" style="color: #333;">file1</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>

</pre>

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<pre style="margin: 0;">-<span id="LC362" 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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">enter_context</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python">                <span class="n" style="color: #333;">_open_single</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC364" 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>

</pre>

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<pre style="margin: 0;">-<span id="LC365" 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>

</pre>

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366

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

367

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC367" 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 class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

368

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC368" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

369

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

370

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC370" 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 class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

371

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC371" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

372

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC372" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

373

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

374

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC374" 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 class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

375

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC375" 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="p">()</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

376

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

377

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC377" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__enter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

378

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC378" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># TODO do not allow this twice</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC379" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

</pre>

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380

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC380" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

381

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC381" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__exit__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

382

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC382" 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="p">()</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC385" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedSequenceAppender</span><span class="p">(</span><span class="n" style="color: #333;">PairedSequenceWriter</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

386

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC386" class="line" lang="python">    <span class="n" style="color: #333;">_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"a"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

387

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

388

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">InterleavedSequenceWriter</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

390

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

391

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"><span class="s" style="color: #d14;">    Write paired-end reads to an interleaved FASTA or FASTQ file</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python">    <span class="n" style="color: #333;">_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"w"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC395" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC396" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

397

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"fastq"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

399

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python">        <span class="n" style="color: #333;">qualities</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

400

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC400" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

401

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC401" class="line" lang="python">    <span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

402

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC402" class="line" lang="python">        <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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC403" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

404

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">writer</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span><span class="p">))</span>  <span class="c1" style="color: #998; font-style: italic;"># only for Mypy</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

405

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC405" 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;">writer</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

406

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC407" 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 class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

408

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC408" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

409

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

410

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC410" 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;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">:</span> <span class="n" style="color: #333;">Sequence</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

411

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC411" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

412

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC412" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC413" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

414

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC414" 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 class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

415

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC415" 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;">close</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

416

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

417

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC417" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__enter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

418

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># TODO do not allow this twice</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

419

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

420

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<pre style="margin: 0;">-<span id="LC420" class="line" lang="python"></span>

</pre>

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421

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__exit__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

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422

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<pre style="margin: 0;">-<span id="LC422" 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="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC423" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC424" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

425

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC425" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">InterleavedSequenceAppender</span><span class="p">(</span><span class="n" style="color: #333;">InterleavedSequenceWriter</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC426" class="line" lang="python">    <span class="n" style="color: #333;">_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"a"</span></span></pre>

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<br>

</li>

<li id="324fa7612afdef67bd89878b1541ef5f20718be0">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#324fa7612afdef67bd89878b1541ef5f20718be0"><strong>src/dnaio/_core.pyi</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>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,7 @@ class Sequence:</td>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">    def __repr__(self) -> str: ...</span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">    def __len__(self) -> int: ...</span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">    def __richcmp__(self, other: Sequence, op: int) -> bool: ...</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">    def qualities_as_bytes(self) -> bytes: ...</span>

</pre>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">    def fastq_bytes(self) -> bytes: ...</span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">    def fastq_bytes_two_headers(self) -> bytes: ...</span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>

</pre>

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<li id="72ff21bf4040f97f9c5919d676e807b4117d01b7">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#72ff21bf4040f97f9c5919d676e807b4117d01b7"><strong>src/dnaio/_core.pyx</strong></a>

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1

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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cython"><span class="c1" style="color: #998; font-style: italic;"># cython: language_level=3, emit_code_comments=False</span></span>

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<td class="new_line diff-line-num" data-linenumber="2" 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="LC2" class="line" lang="cython"></span>

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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cython"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">libc.string</span> <span class="kn" style="font-weight: 600;">cimport</span> <span class="n" style="color: #333;">strncmp</span><span class="p">,</span> <span class="n" style="color: #333;">memcmp</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cython"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cpython.bytes</span> <span class="kn" style="font-weight: 600;">cimport</span> <span class="n" style="color: #333;">PyBytes_FromStringAndSize</span><span class="p">,</span> <span class="n" style="color: #333;">PyBytes_AS_STRING</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cython"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">libc.string</span> <span class="kn" style="font-weight: 600;">cimport</span> <span class="n" style="color: #333;">strncmp</span><span class="p">,</span> <span class="n" style="color: #333;">memcmp</span><span class="p">,</span> <span class="n" style="color: #333;">memcpy</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cython"><span class="kn" style="font-weight: 600;">cimport</span> <span class="nn" style="color: #555;">cython</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cython"></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cython"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastqFormatError</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">@@ -9,9 +10,18 @@ from ._util import shorten</td>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cython"></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cython"><span class="k" style="font-weight: 600;">cdef</span> <span class="kr" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Sequence</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cython">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cython"><span class="s" style="color: #d14;">    A record in a FASTA or FASTQ file. For FASTA, the qualities attribute</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cython"><span class="s" style="color: #d14;">    A sequencing read with read name/id and (optional) qualities</span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cython"></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cython"><span class="s" style="color: #d14;">    If qualities are available, they are as</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cython"><span class="s" style="color: #d14;">    For a Sequence a FASTA file</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cython"><span class="s" style="color: #d14;">    record containing a read in a FASTA or FASTQ file. For FASTA, the qualities attribute</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cython"><span class="s" style="color: #d14;">    is None. For FASTQ, qualities is a string and it contains the qualities</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cython"><span class="s" style="color: #d14;">    encoded as ascii(qual+33).</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cython"><span class="s" style="color: #d14;">    encoded as ASCII(qual+33).</span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cython"></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cython"><span class="s" style="color: #d14;">    Attributes:</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cython"><span class="s" style="color: #d14;">      name (str): The read description</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cython"><span class="s" style="color: #d14;">      sequence (str):</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cython"><span class="s" style="color: #d14;">      qualities (str):</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cython"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cython">    <span class="k" style="font-weight: 600;">cdef</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cython">        <span class="kr" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">str</span> <span class="n" style="color: #333;">name</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">@@ -31,7 +41,13 @@ cdef class Sequence:</td>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cython">                    <span class="n" style="color: #333;">rname</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">qualities</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)))</span></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cython"></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cython">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__getitem__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cython">        <span class="s" style="color: #d14;">"""slicing"""</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cython">        <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cython"><span class="s" style="color: #d14;">        Slice this Sequence. If the qualities attribute is not None, it is</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cython"><span class="s" style="color: #d14;">        sliced accordingly. The read name is copied unchanged.</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cython"></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cython"><span class="s" style="color: #d14;">        Returns:</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cython"><span class="s" style="color: #d14;">          A new Sequence object with a sliced sequence.</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cython"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cython">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">__class__</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cython">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cython">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span><span class="p">[</span><span class="n" style="color: #333;">key</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">@@ -45,6 +61,10 @@ cdef class Sequence:</td>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cython">            <span class="nf" style="color: #900; font-weight: 600;">shorten</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="nf" style="color: #900; font-weight: 600;">shorten</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span><span class="p">),</span> <span class="n" style="color: #333;">qstr</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cython"></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cython">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__len__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cython">        <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cython"><span class="s" style="color: #d14;">        Returns:</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cython"><span class="s" style="color: #d14;">           The number of characters in this sequence</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cython"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cython">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cython"></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cython">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__richcmp__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">op</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="62" 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="82" 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">@@ -62,15 +82,66 @@ cdef class Sequence:</td>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cython">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__reduce__</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="LC83" class="line" lang="cython">        <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="p">(</span><span class="bp" style="color: #999;">self</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;">sequence</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qualities</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cython"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cython">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">qualities_as_bytes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cython">        <span class="s" style="color: #d14;">"""Return the qualities as a bytes object.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cython"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cython"><span class="s" style="color: #d14;">        This is a faster version of qualities.encode('ascii')."""</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cython">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qualities</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cython"></span>

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65

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cython">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fastq_bytes</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="LC66" class="line" lang="cython">        <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'@'</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;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</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;">sequence</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>

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67

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<td class="new_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cython">             <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;">qualities</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

68

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<td class="new_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cython">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cython">        <span class="s" style="color: #d14;">"""Return the entire FASTQ record as bytes which can be written</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cython"><span class="s" style="color: #d14;">        into a file."""</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># Convert to ASCII bytes sequences first as these have a one-to-one</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># relation between size and number of bytes</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># Unlike decoding, ascii is not slower than latin-1. This is because</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># CPython performs a call to PyUnicodeCheck on both occassions. This</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># determines the type of the Unicode object. In fact, the ascii encode</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># is slightly faster because the check for PyASCIIObject is performed</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># first.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bytes</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bytes</span> <span class="n" style="color: #333;">sequence</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;">sequence</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bytes</span> <span class="n" style="color: #333;">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;">qualities</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="104" 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">

104

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">name_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="105" 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">

105

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">sequence_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="106" 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">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">qualities_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="107" 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">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cython"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="108" 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">

108

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># Since Cython will generate code above that is a 100% sure to generate</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="109" 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">

109

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># bytes objects, we can call Python C-API functions that don't perform</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="110" 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">

110

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># checks on the object.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="111" 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">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">name_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">PyBytes_AS_STRING</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="112" 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">

112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sequence_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">PyBytes_AS_STRING</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="113" 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">

113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qualities_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">PyBytes_AS_STRING</span><span class="p">(</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="114" 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">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cython"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="115" 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">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># Total size is name + sequence + qualities + 4 newlines + '+' and an</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="116" 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">

116

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># '@' to be put in front of the name.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="117" 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">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">total_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name_length</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sequence_length</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">qualities_length</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">6</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="118" 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">

118

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cython"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># This is the canonical way to create an uninitialized bytestring of given size</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bytes</span> <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">PyBytes_FromStringAndSize</span><span class="p">(</span><span class="n" style="color: #333;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">total_size</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="121" 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">

121

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">retval_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">PyBytes_AS_STRING</span><span class="p">(</span><span class="n" style="color: #333;">retval</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="122" 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">

122

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC122" class="line" lang="cython"></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="123" 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">

123

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cython">        <span class="c1" style="color: #998; font-style: italic;"># Write the sequences into the bytestring at the correct positions.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="124" 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">

124

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cython">        <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">cursor</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="125" 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">

125

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cython">        <span class="kt" style="color: #458; font-weight: 600;">retval_ptr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">b</span><span class="s" style="color: #d14;">"@"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="126" 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">

126

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cython">        <span class="nf" style="color: #900; font-weight: 600;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">retval_ptr</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">name_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">name_length</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="127" 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">

127

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cython">        <span class="n" style="color: #333;">cursor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name_length</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="128" 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">

128

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cython">        <span class="kt" style="color: #458; font-weight: 600;">retval_ptr</span><span class="p">[</span><span class="n" style="color: #333;">cursor</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">b</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span> <span class="n" style="color: #333;">cursor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="129" 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">

129

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cython">        <span class="nf" style="color: #900; font-weight: 600;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">retval_ptr</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cursor</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_length</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="130" 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">

130

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cython">        <span class="n" style="color: #333;">cursor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sequence_length</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="131" 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">

131

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cython">        <span class="kt" style="color: #458; font-weight: 600;">retval_ptr</span><span class="p">[</span><span class="n" style="color: #333;">cursor</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">b</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span> <span class="n" style="color: #333;">cursor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="132" 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">

132

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cython">        <span class="kt" style="color: #458; font-weight: 600;">retval_ptr</span><span class="p">[</span><span class="n" style="color: #333;">cursor</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">b</span><span class="s" style="color: #d14;">"+"</span><span class="p">;</span> <span class="n" style="color: #333;">cursor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="133" 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">

133

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cython">        <span class="kt" style="color: #458; font-weight: 600;">retval_ptr</span><span class="p">[</span><span class="n" style="color: #333;">cursor</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">b</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span> <span class="n" style="color: #333;">cursor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="134" 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">

134

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC134" class="line" lang="cython">        <span class="nf" style="color: #900; font-weight: 600;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">retval_ptr</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cursor</span><span class="p">,</span> <span class="n" style="color: #333;">qualities_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">qualities_length</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="135" 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">

135

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC135" class="line" lang="cython">        <span class="n" style="color: #333;">cursor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">qualities_length</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="69" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="136" 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">

136

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC136" class="line" lang="cython">        <span class="kt" style="color: #458; font-weight: 600;">retval_ptr</span><span class="p">[</span><span class="n" style="color: #333;">cursor</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">b</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cython">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">retval</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cython"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cython">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fastq_bytes_two_headers</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="LC71" class="line" lang="cython">        <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'@'</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;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</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;">sequence</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+'</span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cython">             <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;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</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;">qualities</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</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="LC73" class="line" lang="cython">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cython">        <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cython"><span class="s" style="color: #d14;">        Return this record in FASTQ format as a bytes object where the header (after the @) is</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cython"><span class="s" style="color: #d14;">        repeated on the third line.</span></span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cython"><span class="s" style="color: #d14;">        """</span></span>

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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cython">        <span class="k" style="font-weight: 600;">return</span> <span class="sa">f</span><span class="s" style="color: #d14;">"@</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="si" style="color: #d14;">}</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span><span class="si" style="color: #d14;">}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="si" style="color: #d14;">}</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qualities</span><span class="si" style="color: #d14;">}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">"ascii"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cython"></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cython"></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cython"><span class="c1" style="color: #998; font-style: italic;"># It would be nice to be able to have the first parameter be an</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="202" 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="273" 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">@@ -202,6 +273,11 @@ def fastq_iter(file, sequence_class, Py_ssize_t buffer_size):</td>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cython">            <span class="n" style="color: #333;">name_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">endskip</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">record_start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cython">            <span class="n" style="color: #333;">name_encoded</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c_buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">record_start</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cython">            <span class="c1" style="color: #998; font-style: italic;"># .decode('latin-1') is 50% faster than .decode('ascii')</span></span>

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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cython">            <span class="c1" style="color: #998; font-style: italic;"># This is because PyUnicode_DecodeLatin1 is an alias for</span></span>

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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cython">            <span class="c1" style="color: #998; font-style: italic;"># _PyUnicode_FromUCS1. Which directly copies the bytes into a</span></span>

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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cython">            <span class="c1" style="color: #998; font-style: italic;"># string object. No operations are taking place. With</span></span>

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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cython">            <span class="c1" style="color: #998; font-style: italic;"># PyUnicode_DecodeASCII, all characters are checked whether they</span></span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cython">            <span class="c1" style="color: #998; font-style: italic;"># exceed 128.</span></span>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cython">            <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">record_start</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">endskip</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">'latin-1'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cython"></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cython">            <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<li id="e5795f7640126a0eb096e91cf0373d32d878161f">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#e5795f7640126a0eb096e91cf0373d32d878161f"><strong>src/dnaio/_util.py</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,6 +5,7 @@ def _is_path(obj: object) -> bool:</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC6" 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="LC7" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># TODO</span></span>

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<pre style="margin: 0;"> <span id="LC9" 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="LC10" 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="LC11" class="line" lang="python">    <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<li id="176822612ada6c351a79b7da6087bb1f3e38c551">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#176822612ada6c351a79b7da6087bb1f3e38c551"><strong>src/dnaio/exceptions.py</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,16 +13,22 @@ class FileFormatError(Exception):</td>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span>  <span class="c1" style="color: #998; font-style: italic;"># starts at 0!</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="new_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python">        <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left">'</span>unknown line<span class="idiff">'</span></span> <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;">line</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;"><span class="idiff">'</span>line {<span class="idiff">}'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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<td class="new_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;"><span class="idiff left">'</span>Error in {<span class="idiff">} file at {}: {}'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">message</span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">        <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left">"</span>unknown line<span class="idiff">"</span></span> <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;">line</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="sa"><span class="idiff">f</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span>line </span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="sa"><span class="idiff left">f</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span>Error in </span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff"> file at </span></span><span class="si" style="color: #d14;"><span class="idiff">{</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff">: </span></span><span class="si" style="color: #d14;"><span class="idiff">{</span></span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">message</span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="18" 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">

18

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<td class="new_line diff-line-num" data-linenumber="18" 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">

18

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="19" 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">

19

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<td class="new_line diff-line-num" data-linenumber="19" 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">

19

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="20" 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="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastqFormatError</span><span class="p">(</span><span class="n" style="color: #333;">FileFormatError</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="python">    <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'FASTQ'</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="22" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="21" 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">

21

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;">    The FASTQ file is not formatted correctly</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="22" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="23" 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">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="22" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">    <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"FASTQ"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<td class="new_line diff-line-num" data-linenumber="25" 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">

25

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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<td class="new_line diff-line-num" data-linenumber="27" 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">

27

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastaFormatError</span><span class="p">(</span><span class="n" style="color: #333;">FileFormatError</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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<td class="new_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="python">    <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'FASTA'</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="28" 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">

28

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="29" 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">

29

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;">    The FASTA file is not formatted correctly</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="30" 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">

30

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="31" 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">

31

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">    <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"FASTA"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="26" 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">

26

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<td class="new_line diff-line-num" 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">

32

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="27" 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">

27

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<td class="new_line diff-line-num" data-linenumber="33" 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">

33

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="28" 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">

28

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<td class="new_line diff-line-num" data-linenumber="34" 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">

34

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">UnknownFileFormat</span><span class="p">(</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">):</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="7af161688a569301ddcba97224af13ce910580cc">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#7af161688a569301ddcba97224af13ce910580cc"><strong>src/dnaio/interfaces.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="1" 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">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ABC</span><span class="p">,</span> <span class="n" style="color: #333;">abstractmethod</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">typing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Iterator</span><span class="p">,</span> <span class="n" style="color: #333;">Tuple</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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;">dnaio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Sequence</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" 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">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="6" 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">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="7" 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">

7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SingleEndReader</span><span class="p">(</span><span class="n" style="color: #333;">ABC</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" 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">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" 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">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" 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 class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Iterator</span><span class="p">[</span><span class="n" style="color: #333;">Sequence</span><span class="p">]:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" 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">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="11" 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">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="13" 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">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedEndReader</span><span class="p">(</span><span class="n" style="color: #333;">ABC</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="14" 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">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="15" 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">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Iterator</span><span class="p">[</span><span class="n" style="color: #333;">Tuple</span><span class="p">[</span><span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="p">]]:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="16" 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">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" 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">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="18" 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">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="19" 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">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SingleEndWriter</span><span class="p">(</span><span class="n" style="color: #333;">ABC</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="20" 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">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="21" 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">

21

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" 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;">record</span><span class="p">:</span> <span class="n" style="color: #333;">Sequence</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="22" 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">

22

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="23" 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">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedEndWriter</span><span class="p">(</span><span class="n" style="color: #333;">ABC</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC27" 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;">record1</span><span class="p">:</span> <span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">record2</span><span class="p">:</span> <span class="n" style="color: #333;">Sequence</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span></pre>

</td>

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<br>

</li>

<li id="a66e9807f4b39aaa61baab58ad1a281bd6691999">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#a66e9807f4b39aaa61baab58ad1a281bd6691999"><strong>src/dnaio/pairedend.py</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">contextlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ExitStack</span></span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PathLike</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">typing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Union</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">,</span> <span class="n" style="color: #333;">Optional</span><span class="p">,</span> <span class="n" style="color: #333;">Iterator</span><span class="p">,</span> <span class="n" style="color: #333;">Tuple</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="5" 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">

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;">xopen</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">xopen</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="6" 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">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="7" 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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">record_names_match</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="8" 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">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FileFormatError</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="9" 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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.interfaces</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PairedEndReader</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndWriter</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="10" 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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.readers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastqReader</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="11" 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">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.writers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.singleend</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_open_single</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="13" 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">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>

</pre>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TwoFilePairedEndReader</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndReader</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="16" 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">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">    Read paired-end reads from two files.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">    Wraps two BinaryFileReader instances, making sure that reads are properly</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="20" 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">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">    paired.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="21" 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">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="22" 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">

22

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="23" 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">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">    <span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="24" 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">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">        <span class="n" style="color: #333;">file1</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="28" 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">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">        <span class="n" style="color: #333;">file2</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="29" 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">

29

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">        <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="30" 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">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="31" 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">

31

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="32" 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">

32

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="python">    <span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">ExitStack</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">stack</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader1</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;">enter_context</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="python">                <span class="n" style="color: #333;">_open_single</span><span class="p">(</span><span class="n" style="color: #333;">file1</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>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="python">            <span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader2</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;">enter_context</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python">                <span class="n" style="color: #333;">_open_single</span><span class="p">(</span><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>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python">            <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;">_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="LC41" 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="LC42" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC43" 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 class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</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="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">(file1=</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader1</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">, file2=</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader2</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">)"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC46" 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 class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Iterator</span><span class="p">[</span><span class="n" style="color: #333;">Tuple</span><span class="p">[</span><span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="p">]]:</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">+<span id="LC48" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Avoid usage of zip() below since it will consume one item too many.</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python">        <span class="n" style="color: #333;">it1</span><span class="p">,</span> <span class="n" style="color: #333;">it2</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;">reader1</span><span class="p">),</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;">reader2</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python">                <span class="n" style="color: #333;">r1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">it1</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">StopIteration</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="56" 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">

56

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># End of file 1. Make sure that file 2 is also at end.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="57" 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">

57

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="58" 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">

58

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">it2</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="59" 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">

59

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC59" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">(</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="60" 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">

60

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC60" class="line" lang="python">                        <span class="s" style="color: #d14;">"Reads are improperly paired. There are more reads in "</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="61" 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">

61

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python">                        <span class="s" style="color: #d14;">"file 2 than in file 1."</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="62" 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">

62

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python">                        <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="63" 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">

63

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC63" class="line" lang="python">                    <span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="64" 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">

64

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC64" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">StopIteration</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="65" 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">

65

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python">                    <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="66" 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">

66

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="67" 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">

67

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="68" 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">

68

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC68" class="line" lang="python">                <span class="n" style="color: #333;">r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">it2</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="69" 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">

69

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC69" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">StopIteration</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="70" 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">

70

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC70" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">(</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="71" 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">

71

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC71" class="line" lang="python">                    <span class="s" style="color: #d14;">"Reads are improperly paired. There are more reads in "</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC72" class="line" lang="python">                    <span class="s" style="color: #d14;">"file 1 than in file 2."</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="73" 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">

73

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC73" class="line" lang="python">                    <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="74" 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">

74

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">                <span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">record_names_match</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">                    <span class="sa">f</span><span class="s" style="color: #d14;">"Reads are improperly paired. Read name '</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">' "</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">                    <span class="sa">f</span><span class="s" style="color: #d14;">"in file 1 does not match '</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">' in file 2."</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">                    <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">                <span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="81" 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">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC83" 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 class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="84" 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">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_close</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="85" 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">

85

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__enter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

88

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__exit__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exc</span><span class="p">):</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

90

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC90" 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="p">()</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

91

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">InterleavedPairedEndReader</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndReader</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="s" style="color: #d14;">    Read paired-end reads from an interleaved FASTQ file.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python">    <span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="103" 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">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python">        <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python">    <span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python">        <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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">reader</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">FastaReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastqReader</span><span class="p">))</span>  <span class="c1" style="color: #998; font-style: italic;"># for Mypy</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC109" 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;">reader</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC110" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</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="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">(</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reader</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">)"</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC115" 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 class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Iterator</span><span class="p">[</span><span class="n" style="color: #333;">Tuple</span><span class="p">[</span><span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="p">]]:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC116" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="117" 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">

117

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<pre style="margin: 0;">+<span id="LC117" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="119" 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">

119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python">                <span class="n" style="color: #333;">r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">StopIteration</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python">                    <span class="s" style="color: #d14;">"Interleaved input file incomplete: Last record "</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python">                    <span class="sa">f</span><span class="s" style="color: #d14;">"'</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">' has no partner."</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python">                    <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python">                <span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">record_names_match</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python">                    <span class="sa">f</span><span class="s" style="color: #d14;">"Reads are improperly paired. Name '</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">' "</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="129" 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">

129

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python">                    <span class="sa">f</span><span class="s" style="color: #d14;">"(first) does not match '</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">' (second)."</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="130" 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">

130

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python">                    <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="131" 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">

131

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python">                <span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="132" 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">

132

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="133" 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">

133

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="134" 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">

134

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<pre style="margin: 0;">+<span id="LC134" 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 class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="135" 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">

135

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<pre style="margin: 0;">+<span id="LC135" 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="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="136" 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">

136

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="137" 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">

137

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__enter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="138" 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">

138

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="139" 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">

139

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="140" 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">

140

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__exit__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="141" 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">

141

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<pre style="margin: 0;">+<span id="LC141" 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="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="142" 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">

142

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TwoFilePairedEndWriter</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndWriter</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="145" 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">

145

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="146" 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">

146

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="147" 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">

147

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python">        <span class="n" style="color: #333;">file1</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python">        <span class="n" style="color: #333;">file2</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="149" 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">

149

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python">        <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="150" 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">

150

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"fastq"</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="151" 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">

151

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python">        <span class="n" style="color: #333;">qualities</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="152" 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">

152

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="153" 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">

153

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python">        <span class="n" style="color: #333;">append</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python">    <span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="155" 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">

155

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python">        <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"a"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">append</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"w"</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="156" 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">

156

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">ExitStack</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">stack</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="157" 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">

157

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<pre style="margin: 0;">+<span id="LC157" 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;">Union</span><span class="p">[</span><span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="158" 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">

158

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<pre style="margin: 0;">+<span id="LC158" 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;">Union</span><span class="p">[</span><span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC159" 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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">enter_context</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="160" 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">

160

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python">                <span class="n" style="color: #333;">_open_single</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python">                    <span class="n" style="color: #333;">file1</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python">                    <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>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="163" 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">

163

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python">                    <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>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="164" 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">

164

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python">                    <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mode</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="165" 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">

165

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python">                    <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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="166" 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">

166

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python">                <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="167" 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">

167

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python">            <span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="168" 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">

168

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<pre style="margin: 0;">+<span id="LC168" 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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">enter_context</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="169" 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">

169

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python">                <span class="n" style="color: #333;">_open_single</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="170" 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">

170

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python">                    <span class="n" style="color: #333;">file2</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="171" 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">

171

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python">                    <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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="172" 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">

172

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python">                    <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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="173" 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">

173

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python">                    <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mode</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="174" 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">

174

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python">                    <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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="175" 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">

175

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python">                <span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="176" 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">

176

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python">            <span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="177" 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">

177

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<pre style="margin: 0;">+<span id="LC177" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="178" 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">

178

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="179" 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">

179

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<pre style="margin: 0;">+<span id="LC179" 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 class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="180" 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">

180

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</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="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">(</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_writer1</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">, </span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_writer2</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">)"</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="181" 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">

181

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="182" 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">

182

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<pre style="margin: 0;">+<span id="LC182" 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 class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC183" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC184" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC186" 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 class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="187" 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">

187

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<pre style="margin: 0;">+<span id="LC187" 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="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="188" 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">

188

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__enter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="190" 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">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># TODO do not allow this twice</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="191" 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">

191

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="192" 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">

192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__exit__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="194" 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">

194

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<pre style="margin: 0;">+<span id="LC194" 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="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">InterleavedPairedEndWriter</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndWriter</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"><span class="s" style="color: #d14;">    Write paired-end reads to an interleaved FASTA or FASTQ file</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python">        <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"fastq"</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python">        <span class="n" style="color: #333;">qualities</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python">        <span class="n" style="color: #333;">append</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python">    <span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python">        <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"a"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">append</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"w"</span></span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python">        <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="LC213" 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="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>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python">        <span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">writer</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span><span class="p">))</span>  <span class="c1" style="color: #998; font-style: italic;"># only for Mypy</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC216" 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;">writer</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC218" 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 class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</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="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">(</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_writer</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">)"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC221" 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;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">:</span> <span class="n" style="color: #333;">Sequence</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC222" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC223" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC225" 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 class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC226" 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;">close</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__enter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># TODO do not allow this twice</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__exit__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC233" 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="p">()</span></span></pre>

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<br>

</li>

<li id="79bba35b6cf4519cc3ab15da71893164d46ad480">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#79bba35b6cf4519cc3ab15da71893164d46ad480"><strong>src/dnaio/readers.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_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="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">@@ -7,9 +7,11 @@ import io</td>

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7

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">typing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Union</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">,</span> <span class="n" style="color: #333;">Optional</span><span class="p">,</span> <span class="n" style="color: #333;">Iterator</span><span class="p">,</span> <span class="n" style="color: #333;">List</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">xopen</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">xopen</span></span>

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<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fastq_iter</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">_fastq_iter</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">shorten</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">_shorten</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaFormatError</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.interfaces</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SingleEndReader</span></span>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="16" 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="LC16" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="17" 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="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BinaryFileReader</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,7 +22,9 @@ class BinaryFileReader:</td>

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<td class="old_line diff-line-num" data-linenumber="20" 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="LC22" class="line" lang="python">    <span class="n" style="color: #333;">paired</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python">    <span class="n" style="color: #333;">mode</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'rb'</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</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;">xopen</span><span class="p">,</span> <span class="n" style="color: #333;">_close_file</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</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;">xopen</span><span class="p">,</span> <span class="n" style="color: #333;">_close_file</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">    <span class="p">):</span></span>

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<td class="new_line diff-line-num" data-linenumber="28" 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="LC28" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;">        The file is a path or a file-like object. In both cases, the file may</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;">        be compressed (.gz, .bz2, .xz).</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">@@ -35,7 +39,7 @@ class BinaryFileReader:</td>

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<pre style="margin: 0;"> <span id="LC39" 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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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC41" 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 class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"{<span class="idiff left">}({!r})"</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></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 class="idiff">,</span></span><span class="idiff"> </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;"><span class="idiff">"</span>name<span class="idiff">"</span></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 class="idiff right">)</span></span></span>

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="sa"><span class="idiff left">f</span></span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</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="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff">('</span></span><span class="si" style="color: #d14;"><span class="idiff">{</span></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;"><span class="idiff">'</span>name<span class="idiff">'</span></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="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff right">')"</span></span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC44" 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 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="LC45" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="51" 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="55" 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">@@ -51,7 +55,7 @@ class BinaryFileReader:</td>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</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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<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastaReader</span><span class="p">(</span><span class="n" style="color: #333;">BinaryFileReader</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastaReader</span><span class="p">(</span><span class="n" style="color: #333;">BinaryFileReader</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">SingleEndReader</span></span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;">    Reader for FASTA files.</span></span>

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<td class="old_line diff-line-num" data-linenumber="57" 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="LC61" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" 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="63" 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">@@ -59,6 +63,7 @@ class FastaReader(BinaryFileReader):</td>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python">        <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python">        <span class="n" style="color: #333;">keep_linebreaks</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python">        <span class="n" style="color: #333;">sequence_class</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Sequence</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" 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="103" 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">@@ -98,8 +103,7 @@ class FastaReader(BinaryFileReader):</td>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python">                <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="104" 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="LC104" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="new_line diff-line-num" data-linenumber="105" 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="LC105" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FastaFormatError</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python">                    <span class="s" style="color: #d14;">"Expected '>' at beginning of record, but got {!r}."</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python">                    <span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">_shorten</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)),</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python">                    <span class="sa">f</span><span class="s" style="color: #d14;">"Expected '>' at beginning of record, but got '</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">_shorten</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'."</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="107" 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="LC107" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</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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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequence_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;">_delimiter</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">),</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="107" 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="111" 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">@@ -107,7 +111,7 @@ class FastaReader(BinaryFileReader):</td>

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<td class="old_line diff-line-num" data-linenumber="107" 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="LC111" class="line" lang="python">        <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">detach</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="109" 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="LC113" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastqReader</span><span class="p">(</span><span class="n" style="color: #333;">BinaryFileReader</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastqReader</span><span class="p">(</span><span class="n" style="color: #333;">BinaryFileReader</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">SingleEndReader</span></span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="115" 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="LC115" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="116" 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="LC116" class="line" lang="python"><span class="s" style="color: #d14;">    Reader for FASTQ files. Does not support multi-line FASTQ files.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="117" 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="LC117" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" 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="119" 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">@@ -115,6 +119,7 @@ class FastqReader(BinaryFileReader):</td>

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<td class="old_line diff-line-num" data-linenumber="115" 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="LC119" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="121" 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="LC121" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python">        <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">        <span class="n" style="color: #333;">sequence_class</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Sequence</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="124" 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="LC124" class="line" lang="python">        <span class="n" style="color: #333;">buffer_size</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1048576</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="125" 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="LC125" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

</pre>

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<br>

</li>

<li id="09b1291e3cfc7a40be592455cb1acaacfa12b950">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#09b1291e3cfc7a40be592455cb1acaacfa12b950"><strong>src/dnaio/singleend.py</strong></a>

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1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">functools</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">typing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Optional</span><span class="p">,</span> <span class="n" style="color: #333;">Union</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" 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">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">UnknownFileFormat</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="6" 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">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.readers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastqReader</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="7" 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">

7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.writers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" 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">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_is_path</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" 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">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" 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">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" 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">

11

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" 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>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="python">    <span class="n" style="color: #333;">file_or_path</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" 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">

13

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="python">    <span class="n" style="color: #333;">opener</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="14" 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">

14

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="python">    <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" 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">

15

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="python">    <span class="n" style="color: #333;">fileformat</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" 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">

16

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">    <span class="n" style="color: #333;">mode</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"r"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" 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">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">    <span class="n" style="color: #333;">qualities</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" 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">

18

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="n" style="color: #333;">FastaReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span><span class="p">]:</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">    Open a single sequence file. See description of open() above.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC23" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">    <span class="n" style="color: #333;">path</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_is_path</span><span class="p">(</span><span class="n" style="color: #333;">file_or_path</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">        <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">fspath</span><span class="p">(</span><span class="n" style="color: #333;">file_or_path</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># type: ignore</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</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="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">file_or_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"readinto"</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">                <span class="s" style="color: #d14;">"When passing in an open file-like object, it must have been opened in binary mode"</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">            <span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC35" 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;">file_or_path</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python">            <span class="n" style="color: #333;">path</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;">name</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python">            <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC40" 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;">False</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python">    <span class="n" style="color: #333;">fastq_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastqReader</span> <span class="k" style="font-weight: 600;">if</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="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">FastqWriter</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python">    <span class="n" style="color: #333;">fasta_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaReader</span> <span class="k" style="font-weight: 600;">if</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="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">FastaWriter</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python">    <span class="n" style="color: #333;">handlers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python">        <span class="s" style="color: #d14;">"fastq"</span><span class="p">:</span> <span class="n" style="color: #333;">functools</span><span class="p">.</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">fastq_handler</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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python">        <span class="s" style="color: #d14;">"fasta"</span><span class="p">:</span> <span class="n" style="color: #333;">functools</span><span class="p">.</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">fasta_handler</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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python">    <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileformat</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python">            <span class="n" style="color: #333;">handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">handlers</span><span class="p">[</span><span class="n" style="color: #333;">fileformat</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python">            <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">UnknownFileFormat</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python">                <span class="sa">f</span><span class="s" style="color: #d14;">"File format '</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fileformat</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">' is unknown (expected 'fasta' or 'fastq')."</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python">            <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;">return</span> <span class="n" style="color: #333;">handler</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_detect_format_from_name</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileformat</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"w"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">qualities</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>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Format not recognized, but we know whether to use a format with or without qualities</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"fastq"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qualities</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"fasta"</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</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="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">fileformat</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python">        <span class="n" style="color: #333;">fileformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_detect_format_from_content</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileformat</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python">            <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python">            <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">UnknownFileFormat</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python">                <span class="sa">f</span><span class="s" style="color: #d14;">"Could not determine whether file '</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">' is FASTA or FASTQ. The file extension "</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python">                <span class="s" style="color: #d14;">"is not available or not recognized, and the first character in the file is "</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="71" 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">

71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python">                <span class="s" style="color: #d14;">"unexpected."</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python">            <span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="73" 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">

73

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="74" 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">

74

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileformat</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="75" 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">

75

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"w"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="76" 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">

76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python">        <span class="n" style="color: #333;">extra</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" because the output file name is not available"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="78" 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">

78

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">UnknownFileFormat</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="79" 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">

79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">            <span class="s" style="color: #d14;">"Auto-detection of the output file format (FASTA/FASTQ) failed"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">extra</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="80" 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">

80

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">        <span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="81" 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">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="82" 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">

82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileformat</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"fastq"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">mode</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"wa"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">qualities</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="83" 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">

83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="84" 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">

84

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<pre style="margin: 0;">+<span id="LC84" 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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="85" 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">

85

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC85" class="line" lang="python">            <span class="s" style="color: #d14;">"Output format cannot be FASTQ since no quality values are available."</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

86

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC86" class="line" lang="python">        <span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="87" 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">

87

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

88

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">handlers</span><span class="p">[</span><span class="n" style="color: #333;">fileformat</span><span class="p">](</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

89

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_detect_format_from_name</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;">    name -- file name</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="s" style="color: #d14;">    Return 'fasta', 'fastq' or None if the format could not be detected.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python">    <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ext</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">".xz"</span><span class="p">,</span> <span class="s" style="color: #d14;">".bz2"</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="n" style="color: #333;">ext</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python">            <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="p">[:</span> <span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">ext</span><span class="p">)]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python">            <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python">    <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ext</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">".fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">".fa"</span><span class="p">,</span> <span class="s" style="color: #d14;">".fna"</span><span class="p">,</span> <span class="s" style="color: #d14;">".csfasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">".csfa"</span><span class="p">]:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"fasta"</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">ext</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">".fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">".fq"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".txt"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"_sequence"</span><span class="p">)):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"fastq"</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="108" 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">

108

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="109" 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">

109

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_detect_format_from_content</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="111" 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">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"><span class="s" style="color: #d14;">    Return 'fasta', 'fastq' or None</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="114" 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">

114

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<pre style="margin: 0;">+<span id="LC114" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="115" 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">

115

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<pre style="margin: 0;">+<span id="LC115" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC116" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="117" 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">

117

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<pre style="margin: 0;">+<span id="LC117" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC119" 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 class="c1" style="color: #998; font-style: italic;"># type: ignore</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="120" 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">

120

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<pre style="margin: 0;">+<span id="LC120" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python">        <span class="sa">b</span><span class="s" style="color: #d14;">"@"</span><span class="p">:</span> <span class="s" style="color: #d14;">"fastq"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="122" 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">

122

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python">        <span class="sa">b</span><span class="s" style="color: #d14;">">"</span><span class="p">:</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python">        <span class="sa">b</span><span class="s" style="color: #d14;">"#"</span><span class="p">:</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;"># Some FASTA variants allow comments</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python">        <span class="sa">b</span><span class="s" style="color: #d14;">""</span><span class="p">:</span> <span class="s" style="color: #d14;">"fastq"</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;"># Pretend FASTQ for empty input</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python">    <span class="p">}</span></span>

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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">formats</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">first_char</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span></pre>

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<br>

</li>

<li id="2c796bdd402f95103c9d6524cf0927843f28bec8">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#2c796bdd402f95103c9d6524cf0927843f28bec8"><strong>src/dnaio/writers.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,12 +5,14 @@ from xopen import xopen</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Sequence</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_is_path</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.interfaces</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SingleEndWriter</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FileWriter</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python">        <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python">        <span class="n" style="color: #333;">_close_file</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python">    <span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +24,7 @@ class FileWriter:</td>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="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>

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"{<span class="idiff left">}({!r})"</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></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 class="idiff">,</span></span><span class="idiff"> </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;"><span class="idiff">"</span>name<span class="idiff">"</span></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 class="idiff right">)</span></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="sa"><span class="idiff left">f</span></span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</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="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff">('</span></span><span class="si" style="color: #d14;"><span class="idiff">{</span></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;"><span class="idiff">'</span>name<span class="idiff">'</span></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="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff right">')"</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="27" 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="LC29" 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 class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC30" 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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" 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">@@ -37,7 +39,7 @@ class FileWriter:</td>

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<pre style="margin: 0;"> <span id="LC39" 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="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastaWriter</span><span class="p">(</span><span class="n" style="color: #333;">FileWriter</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastaWriter</span><span class="p">(</span><span class="n" style="color: #333;">FileWriter</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">SingleEndWriter</span></span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="43" 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="LC43" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;">    Write FASTA-formatted sequences to a file.</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="45" 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="LC45" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" 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="47" 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">@@ -45,6 +47,7 @@ class FastaWriter(FileWriter):</td>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python">        <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python">        <span class="n" style="color: #333;">line_length</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="52" 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="LC52" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="53" 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="LC53" class="line" lang="python">        <span class="n" style="color: #333;">_close_file</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" 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="60" 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">@@ -57,7 +60,7 @@ class FastaWriter(FileWriter):</td>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="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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<td class="new_line diff-line-num" data-linenumber="61" 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="LC61" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC62" 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 class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

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<td class="new_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"FastaWriter('{<span class="idiff left">}')"</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></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;"><span class="idiff">"</span>name<span class="idiff">"</span></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 class="idiff right">)</span></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="sa"><span class="idiff left">f</span></span><span class="s" style="color: #d14;">"FastaWriter('</span><span class="si" style="color: #d14;">{</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;"><span class="idiff">'</span>name<span class="idiff">'</span></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="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff right">')"</span></span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="64" 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="LC64" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="65" 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="LC65" 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="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</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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<td class="new_line diff-line-num" data-linenumber="66" 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="LC66" class="line" lang="python">        <span class="s" style="color: #d14;">"""Write an entry to the the FASTA file.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="89" 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="92" 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">@@ -89,31 +92,41 @@ class FastaWriter(FileWriter):</td>

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<pre style="margin: 0;"> <span id="LC92" 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;">write</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">))</span></span>

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<td class="new_line diff-line-num" data-linenumber="93" 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">

93

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="91" 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">

91

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<td class="new_line diff-line-num" data-linenumber="94" 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">

94

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

92

</td>

<td class="new_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastqWriter</span><span class="p">(</span><span class="n" style="color: #333;">FileWriter</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

95

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastqWriter</span><span class="p">(</span><span class="n" style="color: #333;">FileWriter</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">SingleEndWriter</span></span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="93" 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">

93

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<td class="new_line diff-line-num" data-linenumber="96" 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">

96

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC96" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="94" 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">

94

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<td class="new_line diff-line-num" data-linenumber="97" 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">

97

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;">    Write sequences with qualities in FASTQ format.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="95" 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">

95

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<td class="new_line diff-line-num" data-linenumber="98" 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">

98

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

96

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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;">    FASTQ files are formatted like this:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

97

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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;">    @read name</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

98

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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;">    SEQUENCE</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

99

</td>

<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;">    +</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

100

</td>

<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;">    QUALITIS</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="101" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="99" 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">

99

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;">    FASTQ files are formatted like this::</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="101" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="100" 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">

100

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="101" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="101" 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">

101

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"><span class="s" style="color: #d14;">        @read name</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="101" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="102" 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">

102

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;">        AACCGGTT</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="101" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="103" 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">

103

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;">        +</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="101" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="104" 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">

104

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"><span class="s" style="color: #d14;">        FF,:F,,F</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="101" 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">

101

</td>

<td class="new_line diff-line-num" data-linenumber="105" 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">

105

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="102" 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">

102

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<td class="new_line diff-line-num" data-linenumber="106" 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">

106

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC106" class="line" lang="python">    <span class="n" style="color: #333;">file_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'wb'</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="103" 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">

103

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<td class="new_line diff-line-num" data-linenumber="107" 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">

107

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="104" 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="LC108" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="110" 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="LC110" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span> <span class="n" style="color: #333;">Union</span><span class="p">[</span><span class="n" style="color: #333;">PathLike</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python">        <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="112" 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">

112

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python">        <span class="n" style="color: #333;">two_headers</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="113" 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="LC113" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="114" 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="LC114" class="line" lang="python">        <span class="n" style="color: #333;">_close_file</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="115" 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="LC115" class="line" lang="python">    <span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="116" 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="LC116" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="117" 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">

117

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_two_headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">two_headers</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</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;">_write_two_headers</span> <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;">_two_headers</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_write</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># setattr avoids a complaint from Mypy</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python">        <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"write"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_write_two_headers</span> <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;">_two_headers</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_write</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="114" 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">

114

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<td class="new_line diff-line-num" data-linenumber="120" 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">

120

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="121" 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="LC121" 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 class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"FastqWriter('{}')"</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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="sa">f</span><span class="s" style="color: #d14;">"FastqWriter('</span><span class="si" style="color: #d14;">{</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 class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">')"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">:</span> <span class="n" style="color: #333;">Sequence</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;">        Dummy method to make it possible to instantiate this class.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"><span class="s" style="color: #d14;">        The correct write method is assigned in the constructor.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"></span>

</pre>

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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;">_write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">:</span> <span class="n" style="color: #333;">Sequence</span><span class="p">)</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="LC132" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" 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">@@ -130,5 +143,4 @@ class FastqWriter(FileWriter):</td>

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<pre style="margin: 0;"> <span id="LC143" 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;">write</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">fastq_bytes_two_headers</span><span class="p">())</span></span>

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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 class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeseq</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC133" 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;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"@{0:s}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{1:s}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{2:s}</span><span class="se" style="color: #d14;">\n</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>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python">            <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p">).</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">))</span></span></pre>

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<pre style="margin: 0;">+<span id="LC146" 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;">write</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"@</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">name</span><span class="p">:</span><span class="n" style="color: #333;">s</span><span class="si" style="color: #d14;">}</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">sequence</span><span class="p">:</span><span class="n" style="color: #333;">s</span><span class="si" style="color: #d14;">}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">qualities</span><span class="p">:</span><span class="n" style="color: #333;">s</span><span class="si" style="color: #d14;">}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">"ascii"</span><span class="p">))</span></span></pre>

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</li>

<li id="307d17476eda4102236d69ec93ead958067e02d6">

<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/00964d9fc99ded67eb43eb39c9d8f4c745c1076e#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">@@ -11,9 +11,9 @@ from pytest import raises, mark</td>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dnaio</span></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnaio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python">    <span class="n" style="color: #333;">FileFormatError</span><span class="p">,</span> <span class="n" style="color: #333;">FastaFormatError</span><span class="p">,</span> <span class="n" style="color: #333;">FastqFormatError</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python">    <span class="n" style="color: #333;">FastaReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastqReader</span><span class="p">,</span> <span class="n" style="color: #333;">Interleaved<span class="idiff left right">Sequence</span>Reader</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python">    <span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span><span class="p">,</span> <span class="n" style="color: #333;">Interleaved<span class="idiff left right">Sequence</span>Writer</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">PairedSequence</span>Reader</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python">    <span class="n" style="color: #333;">FastaReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastqReader</span><span class="p">,</span> <span class="n" style="color: #333;">Interleaved<span class="idiff left right">PairedEnd</span>Reader</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python">    <span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span><span class="p">,</span> <span class="n" style="color: #333;">Interleaved<span class="idiff left right">PairedEnd</span>Writer</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">TwoFilePairedEnd</span>Reader</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnaio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">record_names_match</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnaio.writers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FileWriter</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">@@ -35,6 +35,14 @@ class TestSequence:</td>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python">            <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"ACGT"</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"#####"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fastq_bytes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"===="</span><span class="p">).</span><span class="n" style="color: #333;">fastq_bytes</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> \</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python">            <span class="sa">b</span><span class="s" style="color: #d14;">"@name</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ACGT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">====</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fastq_bytes_two_headers</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"===="</span><span class="p">).</span><span class="n" style="color: #333;">fastq_bytes_two_headers</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> \</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python">            <span class="sa">b</span><span class="s" style="color: #d14;">"@name</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ACGT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+name</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">====</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="38" 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">

38

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<td class="new_line diff-line-num" data-linenumber="46" 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="LC46" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" data-linenumber="47" 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="LC47" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFastaReader</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="48" 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="LC48" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="329" 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="337" 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">@@ -329,7 +337,7 @@ class TestInterleavedReader:</td>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python">                <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">'read3/2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TGTTATTAATATCAAGTTGG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'#HHHHHHHHHHHHHHHHHHH'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python">            <span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python">        <span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Interleaved<span class="idiff left right">Sequence</span>Reader</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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Interleaved<span class="idiff left right">PairedEnd</span>Reader</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>

</pre>

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<pre style="margin: 0;"> <span id="LC341" 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="LC343" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -340,14 +348,14 @@ class TestInterleavedReader:</td>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_missing_partner</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="LC349" class="line" lang="python">        <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BytesIO</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'@r1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ACG</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">HHH</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="LC350" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FileFormatError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">info</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;">with</span> <span class="n" style="color: #333;">Interleaved<span class="idiff left right">Sequence</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">s</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="LC351" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Interleaved<span class="idiff left right">PairedEnd</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">s</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="LC352" class="line" lang="python">                <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="LC353" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"Interleaved input file incomplete"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">message</span></span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_incorrectly_paired</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="LC356" class="line" lang="python">        <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BytesIO</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'@r1/1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ACG</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">HHH</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">@wrong_name</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">TTT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">HHH</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="LC357" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FileFormatError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">info</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Interleaved<span class="idiff left right">Sequence</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">s</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="LC358" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Interleaved<span class="idiff left right">PairedEnd</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">s</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="LC359" class="line" lang="python">                <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>

</pre>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"Reads are improperly paired"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">message</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="447" 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="455" 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">@@ -447,7 +455,7 @@ class TestInterleavedWriter:</td>

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="python">            <span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python">        <span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python">        <span class="n" style="color: #333;">bio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BytesIO</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC450" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Interleaved<span class="idiff left right">Sequence</span>Writer</span><span class="p">(</span><span class="n" style="color: #333;">bio</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">writer</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Interleaved<span class="idiff left right">PairedEnd</span>Writer</span><span class="p">(</span><span class="n" style="color: #333;">bio</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">writer</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="459" 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="LC459" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">reads</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python">                <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 class="n" style="color: #333;">read2</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="461" 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="LC461" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">bio</span><span class="p">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="462" 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="470" 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">@@ -462,7 +470,7 @@ class TestPairedSequenceReader:</td>

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<pre style="margin: 0;"> <span id="LC470" 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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="471" 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="LC471" class="line" lang="python">        <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BytesIO</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'@r1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ACG</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">HHH</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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<td class="old_line diff-line-num" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="472" 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="LC472" class="line" lang="python">        <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BytesIO</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'@r2</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">GTT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">858</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC465" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;"><span class="idiff left right">PairedSequence</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">psr</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;"><span class="idiff left right">TwoFilePairedEnd</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">psr</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="p">[</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="475" 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="LC475" class="line" lang="python">                <span class="p">(</span><span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">"r1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"HHH"</span><span class="p">),</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">"r2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GTT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"858"</span><span class="p">)),</span></span>

</pre>

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468

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<td class="new_line diff-line-num" data-linenumber="476" 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="LC476" class="line" lang="python">            <span class="p">]</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;">psr</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="500" 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="508" 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">@@ -500,7 +508,7 @@ class TestPairedSequenceReader:</td>

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<td class="old_line diff-line-num" data-linenumber="500" 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="LC508" class="line" lang="python">        <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BytesIO</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'@r1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ACG</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">HHH</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="LC509" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="502" 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="LC510" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FileFormatError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">info</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

503

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<td class="new_line diff-line-num old" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC503" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;"><span class="idiff left right">PairedSequence</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">psr</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;"><span class="idiff left right">TwoFilePairedEnd</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">psr</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="504" 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">

504

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<td class="new_line diff-line-num" data-linenumber="512" 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">

512

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python">                <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">psr</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="513" 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">

513

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<pre style="margin: 0;"> <span id="LC513" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"There are more reads in file 2 than in file 1"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">message</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="514" 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">

514

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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="509" 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="517" 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">@@ -509,7 +517,7 @@ class TestPairedSequenceReader:</td>

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<td class="old_line diff-line-num" data-linenumber="509" 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">

509

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<td class="new_line diff-line-num" data-linenumber="517" 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="LC517" class="line" lang="python">        <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BytesIO</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>

</pre>

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510

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<td class="new_line diff-line-num" data-linenumber="518" 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">

518

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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="519" 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">

519

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FileFormatError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">info</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

512

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<td class="new_line diff-line-num old" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC512" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;"><span class="idiff left right">PairedSequence</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">psr</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;"><span class="idiff left right">TwoFilePairedEnd</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">psr</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="513" 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">

513

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<pre style="margin: 0;"> <span id="LC521" class="line" lang="python">                <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">psr</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="514" 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">

514

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<pre style="margin: 0;"> <span id="LC522" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"There are more reads in file 1 than in file 2"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">message</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="515" 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">

515

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<td class="new_line diff-line-num" data-linenumber="523" 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="LC523" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="517" 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="525" 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">@@ -517,7 +525,7 @@ class TestPairedSequenceReader:</td>

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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python">        <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BytesIO</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'@r1/1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ACG</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">HHH</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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518

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<td class="new_line diff-line-num" data-linenumber="526" 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="LC526" class="line" lang="python">        <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BytesIO</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'@wrong_name</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">TTT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">HHH</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="527" 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="LC527" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FileFormatError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">info</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

520

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<td class="new_line diff-line-num old" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC520" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;"><span class="idiff left right">PairedSequence</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">psr</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="528" 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">

528

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<pre style="margin: 0;">+<span id="LC528" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;"><span class="idiff left right">TwoFilePairedEnd</span>Reader</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">psr</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="521" 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">

521

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<td class="new_line diff-line-num" data-linenumber="529" 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">

529

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<pre style="margin: 0;"> <span id="LC529" class="line" lang="python">                <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">psr</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="522" 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">

522

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<td class="new_line diff-line-num" data-linenumber="530" 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">

530

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"Reads are improperly paired"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">message</span></span>

</pre>

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523

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<td class="new_line diff-line-num" data-linenumber="531" 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">

531

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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python"></span>

</pre>

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